diff --git a/.gitignore b/.gitignore
index 0732b22c45d..b840d6d2513 100644
--- a/.gitignore
+++ b/.gitignore
@@ -280,6 +280,10 @@ package-lock.json
 # jstestfuzz generated test directory
 /jstestfuzz/
 
+# docker volumes mapped in lint_fuzzer_sanity_patch.py
+/jstestfuzzinput
+/jstestfuzzoutput
+
 # Bazel-related work
 # (Note that each string does NOT terminate with a '/' so that gitignore works properly)
 bazel-*
diff --git a/etc/evergreen_yml_components/definitions.yml b/etc/evergreen_yml_components/definitions.yml
index 5a87ece939c..b1bead126c6 100644
--- a/etc/evergreen_yml_components/definitions.yml
+++ b/etc/evergreen_yml_components/definitions.yml
@@ -1812,14 +1812,9 @@ functions:
 
   "setup jstestfuzz":
     - *f_expansions_write
-    - command: github.generate_token
+    - command: ec2.assume_role
       params:
-        owner: 10gen
-        repo: jstestfuzz
-        expansion_name: github_token
-        permissions:
-          metadata: read
-          contents: read
+        role_arn: "arn:aws:iam::901841024863:role/ecr-role-evergreen-ro"
     - command: subprocess.exec
       display_name: "jstestfuzz setup sh"
       params:
@@ -1827,7 +1822,13 @@ functions:
         args:
           - "./src/evergreen/jstestfuzz_setup.sh"
         include_expansions_in_env:
-          - github_token
+          - AWS_ACCESS_KEY_ID
+          - AWS_SECRET_ACCESS_KEY
+          - AWS_SESSION_TOKEN
+    - command: expansions.update
+      params:
+        file: src/expansions.yml
+    - *f_expansions_write
 
   "setup query_tester test repos":
     - *f_expansions_write
@@ -1867,6 +1868,8 @@ functions:
         binary: bash
         args:
           - "src/evergreen/lint_fuzzer_sanity_patch.sh"
+        include_expansions_in_env:
+          - CONTAINER_RUNTIME
 
   "lint fuzzer sanity all":
     - *f_expansions_write
@@ -1876,6 +1879,8 @@ functions:
         binary: bash
         args:
           - "./src/evergreen/lint_fuzzer_sanity_all.sh"
+        include_expansions_in_env:
+          - CONTAINER_RUNTIME
 
   "monitor mongo fork 10gen":
     - *f_expansions_write
@@ -1925,6 +1930,8 @@ functions:
         binary: bash
         args:
           - "./src/evergreen/jstestfuzz_run.sh"
+        include_expansions_in_env:
+          - CONTAINER_RUNTIME
     - command: archive.targz_pack
       display_name: "archive jstests.tgz"
       params:
diff --git a/etc/evergreen_yml_components/tasks/misc_tasks.yml b/etc/evergreen_yml_components/tasks/misc_tasks.yml
index 5cca0f321f6..95cbc1ebba4 100644
--- a/etc/evergreen_yml_components/tasks/misc_tasks.yml
+++ b/etc/evergreen_yml_components/tasks/misc_tasks.yml
@@ -1178,7 +1178,7 @@ tasks:
       - func: "setup jstestfuzz"
       - func: "run jstestfuzz"
         vars:
-          jstestfuzz_vars: "--numGeneratedFiles 2 --jsTestsDir ../jstests"
+          jstestfuzz_vars: "--numGeneratedFiles 2 --jsTestsDir jstests"
           npm_command: "jstestfuzz"
       - func: "get engflow creds"
       - func: "bazel test"
diff --git a/etc/evergreen_yml_components/tasks/resmoke/server_divisions/clusters_and_integrations/tasks.yml b/etc/evergreen_yml_components/tasks/resmoke/server_divisions/clusters_and_integrations/tasks.yml
index d38184217b9..53fd1a33e77 100644
--- a/etc/evergreen_yml_components/tasks/resmoke/server_divisions/clusters_and_integrations/tasks.yml
+++ b/etc/evergreen_yml_components/tasks/resmoke/server_divisions/clusters_and_integrations/tasks.yml
@@ -2455,7 +2455,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_causal_consistency
           resmoke_args: --numClientsPerFixture=10
 
@@ -2480,7 +2480,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 2
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_kill_terminate_stepdown
           resmoke_args: --numClientsPerFixture=10
 
@@ -2509,7 +2509,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 2
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_kill_terminate_stepdown
           resmoke_args: >-
             --numClientsPerFixture=10
@@ -2593,7 +2593,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded
           resmoke_args: --numClientsPerFixture=10
 
@@ -2616,7 +2616,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_notablescan
           resmoke_args: --numClientsPerFixture=10
 
@@ -2638,7 +2638,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_causal_consistency
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -2663,7 +2663,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: 5
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_kill_terminate_stepdown
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -2687,7 +2687,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -2711,7 +2711,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           resmoke_args: >-
             --mongodSetParameters='{logComponentVerbosity: {command: 2}}'
             --runNoFeatureFlagTests
@@ -2734,7 +2734,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_notablescan
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -2756,7 +2756,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_sharded_with_config_transitions_and_add_remove_shard
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
diff --git a/etc/evergreen_yml_components/tasks/resmoke/server_divisions/durable_transactions_and_availability/tasks.yml b/etc/evergreen_yml_components/tasks/resmoke/server_divisions/durable_transactions_and_availability/tasks.yml
index d6eed17eea9..160a002dff2 100644
--- a/etc/evergreen_yml_components/tasks/resmoke/server_divisions/durable_transactions_and_availability/tasks.yml
+++ b/etc/evergreen_yml_components/tasks/resmoke/server_divisions/durable_transactions_and_availability/tasks.yml
@@ -719,7 +719,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication
           resmoke_args: --numClientsPerFixture=10
 
@@ -742,7 +742,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication_notablescan
           resmoke_args: --numClientsPerFixture=10
 
@@ -764,7 +764,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication_write_conflicts
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}' --numClientsPerFixture=10"
 
@@ -789,7 +789,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: 8
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication_fcbis
           resmoke_args: --storageEngine=wiredTiger
           name: jstestfuzz_replication_fcbis
@@ -816,7 +816,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -840,7 +840,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: 8
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication_initsync
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -868,7 +868,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           resmoke_args: >-
             --mongodSetParameters='{logComponentVerbosity: {command: 2}}'
             --runNoFeatureFlagTests
@@ -891,7 +891,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication_notablescan
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -913,7 +913,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication_write_conflicts
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -1841,7 +1841,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_replication
           resmoke_args: >-
             --numClientsPerFixture=10
@@ -2054,7 +2054,7 @@ tasks:
           <<: *jstestfuzz_config_vars
           num_files: ${jstestfuzz_concurrent_num_files|10}
           num_tasks: 5
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz
           resmoke_args: --numClientsPerFixture=10
 
@@ -2076,7 +2076,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_interrupt
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
@@ -2098,7 +2098,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz_interrupt_replication
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
 
diff --git a/etc/evergreen_yml_components/tasks/resmoke/server_divisions/query/tasks.yml b/etc/evergreen_yml_components/tasks/resmoke/server_divisions/query/tasks.yml
index 69394f0828c..75cacc4cac2 100644
--- a/etc/evergreen_yml_components/tasks/resmoke/server_divisions/query/tasks.yml
+++ b/etc/evergreen_yml_components/tasks/resmoke/server_divisions/query/tasks.yml
@@ -433,7 +433,7 @@ tasks:
           suite: generational_fuzzer
           use_large_distro: "true"
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
-          jstestfuzz_vars: --diffTestingMode timeseries --numPipelines=1000 --metaSeed 1726779665485 --jstestfuzzGitRev 8ddd8f12cab0
+          jstestfuzz_vars: --diffTestingMode timeseries --numPipelines=1000 --metaSeed 1726779665485 --jstestfuzzGitRev 8ddd8f12cab0088cfcbef520f248803e17284677
 
   ## Standalone fuzzer for checking block_processing correctness ##
   - <<: *jstestfuzz_template
@@ -1120,7 +1120,7 @@ tasks:
       - func: "generate resmoke tasks"
         vars:
           <<: *jstestfuzz_config_vars
-          jstestfuzz_vars: --jsTestsDir ../jstests
+          jstestfuzz_vars: --jsTestsDir jstests
           suite: jstestfuzz
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
           npm_command: jstestfuzz
@@ -1601,7 +1601,7 @@ tasks:
           resmoke_args: >-
             --mongodSetParameters='{logComponentVerbosity: {command: 2}}'
             --runNoFeatureFlagTests
-          jstestfuzz_vars: --metaSeed 1726779665485 --jstestfuzzGitRev 8ddd8f12cab0
+          jstestfuzz_vars: --metaSeed 1726779665485 --jstestfuzzGitRev 8ddd8f12cab0088cfcbef520f248803e17284677
 
   # jstestfuzz standalone update time-series generational fuzzer ##
   - <<: *jstestfuzz_template
@@ -1853,7 +1853,7 @@ tasks:
           suite: generational_fuzzer
           use_large_distro: "true"
           resmoke_args: "--mongodSetParameters='{logComponentVerbosity: {command: 2}}'"
-          jstestfuzz_vars: --diffTestingMode optimization --metaSeed 1726779665485 --jstestfuzzGitRev 8ddd8f12cab0
+          jstestfuzz_vars: --diffTestingMode optimization --metaSeed 1726779665485 --jstestfuzzGitRev 8ddd8f12cab0088cfcbef520f248803e17284677
 
   - <<: *task_template
     name: aggregation_repeat_queries_multiplan_single_solutions
diff --git a/etc/evergreen_yml_components/variants/windows/test_dev_master_and_lts_branches_only.yml b/etc/evergreen_yml_components/variants/windows/test_dev_master_and_lts_branches_only.yml
index 6e07158eba5..cf58594b3cc 100644
--- a/etc/evergreen_yml_components/variants/windows/test_dev_master_and_lts_branches_only.yml
+++ b/etc/evergreen_yml_components/variants/windows/test_dev_master_and_lts_branches_only.yml
@@ -43,7 +43,8 @@ buildvariants:
       - name: concurrency_replication_causal_consistency_gen
       - name: initial_sync_fuzzer_gen
       - name: .jscore .common !.decimal !.sharding
-      - name: .jstestfuzz .common !.feature_flag_guarded
+      # SERVER-105328: Enable this task once container support is added to Windows variants.
+      # - name: .jstestfuzz .common !.feature_flag_guarded
       - name: .read_write_concern .linearize !.durable_history
       - name: replica_sets_auth_gen
       - name: replica_sets_jscore_passthrough_gen
diff --git a/etc/evergreen_yml_components/variants/wiredtiger/test_dev_master_branch_only.yml b/etc/evergreen_yml_components/variants/wiredtiger/test_dev_master_branch_only.yml
index c39a5142ac3..6de602aa924 100644
--- a/etc/evergreen_yml_components/variants/wiredtiger/test_dev_master_branch_only.yml
+++ b/etc/evergreen_yml_components/variants/wiredtiger/test_dev_master_branch_only.yml
@@ -170,7 +170,8 @@ buildvariants:
         distros:
           - windows-2016-dc
       - name: .jscore .common !.sharding
-      - name: .jstestfuzz .common !.feature_flag_guarded
+      # SERVER-105328: Enable this task once container support is added to Windows variants.
+      # - name: .jstestfuzz .common !.feature_flag_guarded
       - name: replica_sets_auth_gen
       - name: sasl
       - name: sharding_auth_audit_gen
diff --git a/evergreen/jstestfuzz_run.sh b/evergreen/jstestfuzz_run.sh
index 1c7e16c1ab3..adb1d4e7bab 100644
--- a/evergreen/jstestfuzz_run.sh
+++ b/evergreen/jstestfuzz_run.sh
@@ -3,29 +3,16 @@ DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" > /dev/null 2>&1 && pwd)"
 
 set -evo pipefail
 
-cd src/jstestfuzz
-
 # Store 'jstestfuzz_vars' into 'vars'. We will use 'vars' instead of 'jstestfuzz_vars' for
 # the rest of this shell script.
 vars="${jstestfuzz_vars}"
 
-# If the "--jstestfuzzGitRev" option is present in 'vars', copy the option's value into
-# 'jstestfuzz_gitrev' and remove it from 'vars', and then reset the jstestfuzz repo to the
-# specified git revision.
+# # If the "--jstestfuzzGitRev" option is present in 'vars', copy the option's value into
+# # 'jstestfuzz_gitrev' and remove it from 'vars'.
 echo "${vars}" | grep -q -- '--jstestfuzzGitRev[ \t]\+[A-Za-z0-9]\+' && RET=0 || RET=$?
 if [ $RET -eq 0 ]; then
   jstestfuzz_gitrev=$(echo "${vars}" | sed -e 's/.*--jstestfuzzGitRev[ \t]\+\([A-Za-z0-9]\+\).*/\1/')
   vars=$(echo "${vars}" | sed -e 's/\(.*\)--jstestfuzzGitRev[ \t]\+[A-Za-z0-9]\+\(.*\)/\1\2/')
-
-  for i in {1..5}; do
-    git reset --hard "${jstestfuzz_gitrev}" && RET=0 && break || RET=$? && sleep 5
-    echo "Failed to reset jstestfuzz to git revision ${jstestfuzz_gitrev}, retrying..."
-  done
-
-  if [ $RET -ne 0 ]; then
-    echo "Failed to reset jstestfuzz to git revision ${jstestfuzz_gitrev}"
-    exit $RET
-  fi
 fi
 
 # If the "--metaSeed" option is present in 'vars', copy the option's value into 'meta_seed'
@@ -73,4 +60,10 @@ if [[ "${npm_command}" != "jstestfuzz" ]]; then
   maybe_use_es_modules="--useEsModules"
 fi
 
-./src/scripts/npm_run.sh ${npm_command} -- ${vars} ${generated_seed_flag} ${in_patch_build_flag} ${maybe_use_es_modules} --branch ${branch_name}
+mkdir -p ./src/jstestfuzz/out
+
+$CONTAINER_RUNTIME run --rm \
+  -v "./src/jstestfuzz/out:/app/out" \
+  -v "./src/jstests:/app/jstests" \
+  901841024863.dkr.ecr.us-east-1.amazonaws.com/mongodb-internal/jstestfuzz:${jstestfuzz_gitrev:-latest} \
+  npm run-script ${npm_command} -- ${vars} ${generated_seed_flag} ${in_patch_build_flag} ${maybe_use_es_modules} --branch ${branch_name}
diff --git a/evergreen/jstestfuzz_setup.sh b/evergreen/jstestfuzz_setup.sh
index 3c35305b697..fa6e37e2490 100644
--- a/evergreen/jstestfuzz_setup.sh
+++ b/evergreen/jstestfuzz_setup.sh
@@ -6,12 +6,18 @@ cd src
 set -o errexit
 set -o verbose
 
-for i in {1..5}; do
-  git clone https://x-access-token:${github_token}@github.com/10gen/jstestfuzz.git && RET=0 && break || RET=$? && sleep 5
-  echo "Failed to clone github.com:10gen/jstestfuzz.git, retrying..."
-done
+if command -v docker > /dev/null 2>&1; then
+  echo "Docker is installed, using docker"
+  CONTAINER_RUNTIME=docker
 
-if [ $RET -ne 0 ]; then
-  echo "Failed to clone git@github.com:10gen/jstestfuzz.git"
-  exit $RET
+elif command -v podman > /dev/null 2>&1; then
+  echo "Podman is installed, using podman"
+  CONTAINER_RUNTIME=podman
+else
+  echo "Neither Docker nor Podman is installed. Please install one of them."
+  exit 1
 fi
+
+echo "CONTAINER_RUNTIME: ${CONTAINER_RUNTIME}" >> expansions.yml
+
+aws ecr get-login-password --region us-east-1 | $CONTAINER_RUNTIME login --username AWS --password-stdin 901841024863.dkr.ecr.us-east-1.amazonaws.com
diff --git a/evergreen/lint_fuzzer_sanity_all.sh b/evergreen/lint_fuzzer_sanity_all.sh
index 4a4067585c4..d1701af3c20 100644
--- a/evergreen/lint_fuzzer_sanity_all.sh
+++ b/evergreen/lint_fuzzer_sanity_all.sh
@@ -1,22 +1,23 @@
 DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" > /dev/null 2>&1 && pwd)"
 . "$DIR/prelude.sh"
 
-cd src/jstestfuzz
+cd src
 
 set -o pipefail
 set -o verbose
 
-# Run first with help which will do the install
-# Then we can run it in parallel
-./src/scripts/npm_run.sh --help
+LOCAL_INPUT_DIR="$PWD"
+CONTAINER_INPUT_DIR="/app"
+
+# Pull first which will do the install then allow parallel processing below
+podman pull 901841024863.dkr.ecr.us-east-1.amazonaws.com/mongodb-internal/jstestfuzz:latest
 # Run parse-jsfiles on 50 files at a time with 32 processes in parallel.
 # Skip javascript files in third_party directory
-find "$PWD/../jstests" "$PWD/../src/mongo/db/modules/enterprise" -path "$PWD/../jstests/third_party" -prune -o -name "*.js" -print | xargs -P 32 -L 50 ./src/scripts/npm_run.sh parse-jsfiles -- 2>&1 | tee lint_fuzzer_sanity.log
+find "jstests" "src/mongo/db/modules/enterprise" -path "$PWD/jstests/third_party" -prune -o -name "*.js" -print \
+  | xargs -P 32 -L 50 $CONTAINER_RUNTIME run -v $LOCAL_INPUT_DIR/jstests:$CONTAINER_INPUT_DIR/jstests -v $LOCAL_INPUT_DIR/src/mongo/db/modules/enterprise:$CONTAINER_INPUT_DIR/src/mongo/db/modules/enterprise 901841024863.dkr.ecr.us-east-1.amazonaws.com/mongodb-internal/jstestfuzz:latest npm run-script parse-jsfiles -- 2>&1 \
+  | tee lint_fuzzer_sanity.log
 exit_code=$?
 
-# Exit out of the jstestfuzz directory
-cd ..
-
 activate_venv
-$python ./buildscripts/simple_report.py --test-name lint_fuzzer_sanity_all --log-file jstestfuzz/lint_fuzzer_sanity.log --exit-code $exit_code
+$python ./buildscripts/simple_report.py --test-name lint_fuzzer_sanity_all --log-file lint_fuzzer_sanity.log --exit-code $exit_code
 exit $exit_code
diff --git a/evergreen/lint_fuzzer_sanity_patch.py b/evergreen/lint_fuzzer_sanity_patch.py
index 9eb74aa39a0..10dfbe76069 100644
--- a/evergreen/lint_fuzzer_sanity_patch.py
+++ b/evergreen/lint_fuzzer_sanity_patch.py
@@ -40,18 +40,31 @@ for file in diffed_files:
     os.makedirs(copy_dest.parent, exist_ok=True)
     shutil.copy(file, copy_dest)
 
-OUTPUT_FULL_DIR = Path(os.getcwd()) / OUTPUT_DIR
-INPUT_FULL_DIR = Path(os.getcwd()) / INPUT_DIR
+CONTAINER_RUNTIME = os.environ.get("CONTAINER_RUNTIME")
+LOCAL_OUTPUT_FULL_DIR = Path(os.getcwd()) / OUTPUT_DIR
+LOCAL_INPUT_FULL_DIR = Path(os.getcwd()) / INPUT_DIR
+
+CONTAINER_INPUT_PATH = f"/app/{INPUT_DIR}"
+CONTAINER_OUTPUT_PATH = f"/app/{OUTPUT_DIR}"
 
 subprocess.run(
     [
-        "./src/scripts/npm_run.sh",
+        CONTAINER_RUNTIME,
+        "run",
+        "--rm",
+        "-v",
+        f"{LOCAL_INPUT_FULL_DIR}:{CONTAINER_INPUT_PATH}",
+        "-v",
+        f"{LOCAL_OUTPUT_FULL_DIR}:{CONTAINER_OUTPUT_PATH}",
+        "901841024863.dkr.ecr.us-east-1.amazonaws.com/mongodb-internal/jstestfuzz:latest",
+        "npm",
+        "run-script",
         "jstestfuzz",
         "--",
         "--jsTestsDir",
-        INPUT_FULL_DIR,
+        CONTAINER_INPUT_PATH,
         "--out",
-        OUTPUT_FULL_DIR,
+        CONTAINER_OUTPUT_PATH,
         "--numSourceFiles",
         str(min(num_changed_files, 100)),
         "--numGeneratedFiles",
@@ -63,7 +76,6 @@ subprocess.run(
         "10",
     ],
     check=True,
-    cwd="jstestfuzz",
 )
 
 
@@ -73,13 +85,27 @@ def _parse_jsfile(jsfile: Path) -> simple_report.Result:
 
     Returns what should be added to the report given to evergreen
     """
-    print(f"Trying to parse jsfile {jsfile}")
+    # Find the relative path to the jsfile in the volume on the container
+    relative_js_file_path = f"{INPUT_DIR}/{jsfile.relative_to(LOCAL_INPUT_FULL_DIR)}"
     start_time = time.time()
     proc = subprocess.run(
-        ["./src/scripts/npm_run.sh", "parse-jsfiles", "--", str(jsfile)],
+        [
+            CONTAINER_RUNTIME,
+            "run",
+            "--rm",
+            "-v",
+            f"{LOCAL_INPUT_FULL_DIR}:{CONTAINER_INPUT_PATH}",
+            "-v",
+            f"{LOCAL_OUTPUT_FULL_DIR}:{CONTAINER_OUTPUT_PATH}",
+            "901841024863.dkr.ecr.us-east-1.amazonaws.com/mongodb-internal/jstestfuzz:latest",
+            "npm",
+            "run-script",
+            "parse-jsfiles",
+            "--",
+            str(relative_js_file_path),
+        ],
         stdout=subprocess.PIPE,
         stderr=subprocess.STDOUT,
-        cwd="jstestfuzz",
     )
     end_time = time.time()
     status = "pass" if proc.returncode == 0 else "fail"
@@ -104,7 +130,7 @@ report = simple_report.Report(failures=0, results=[])
 with futures.ThreadPoolExecutor() as executor:
     parse_jsfiles_futures = [
         executor.submit(_parse_jsfile, Path(jsfile))
-        for jsfile in glob.iglob(str(OUTPUT_FULL_DIR / "**"), recursive=True)
+        for jsfile in glob.iglob(f"{LOCAL_INPUT_FULL_DIR}/**", recursive=True)
         if os.path.isfile(jsfile)
     ]