diff --git a/tools/pre_commit/shellcheck.baseline b/tools/pre_commit/shellcheck.baseline
new file mode 100644
index 000000000..7433bb331
--- /dev/null
+++ b/tools/pre_commit/shellcheck.baseline
@@ -0,0 +1,89 @@
+benchmarks/auto_tune/auto_tune.sh:SC2034
+benchmarks/auto_tune/auto_tune.sh:SC2086
+benchmarks/auto_tune/batch_auto_tune.sh:SC2086
+benchmarks/run_structured_output_benchmark.sh:SC2028
+benchmarks/run_structured_output_benchmark.sh:SC2034
+benchmarks/run_structured_output_benchmark.sh:SC2086
+.buildkite/image_build/image_build_cpu_arm64.sh:SC2086
+.buildkite/image_build/image_build_cpu.sh:SC2086
+.buildkite/image_build/image_build_hpu.sh:SC2086
+.buildkite/lm-eval-harness/run-lm-eval-chartqa-vllm-vlm-baseline.sh:SC2086
+.buildkite/lm-eval-harness/run-lm-eval-mmlupro-vllm-baseline.sh:SC2034
+.buildkite/performance-benchmarks/scripts/run-performance-benchmarks.sh:SC2027
+.buildkite/performance-benchmarks/scripts/run-performance-benchmarks.sh:SC2086
+.buildkite/performance-benchmarks/scripts/run-performance-benchmarks.sh:SC2126
+.buildkite/scripts/annotate-rocm-release.sh:SC2086
+.buildkite/scripts/cache-rocm-base-wheels.sh:SC2012
+.buildkite/scripts/cherry-pick-from-milestone.sh:SC2064
+.buildkite/scripts/hardware_ci/run-cpu-test-ppc64le.sh:SC2086
+.buildkite/scripts/hardware_ci/run-cpu-test.sh:SC2086
+.buildkite/scripts/hardware_ci/run-hpu-test.sh:SC2086
+.buildkite/scripts/hardware_ci/run-npu-test.sh:SC1090
+.buildkite/scripts/hardware_ci/run-npu-test.sh:SC2006
+.buildkite/scripts/hardware_ci/run-npu-test.sh:SC2086
+.buildkite/scripts/hardware_ci/run-npu-test.sh:SC2181
+.buildkite/scripts/hardware_ci/run-xpu-test.sh:SC2086
+.buildkite/scripts/push-nightly-builds.sh:SC2086
+.buildkite/scripts/run-multi-node-test.sh:SC2086
+.buildkite/scripts/run-multi-node-test.sh:SC2089
+.buildkite/scripts/run-multi-node-test.sh:SC2090
+.buildkite/scripts/run-prime-rl-test.sh:SC2086
+.buildkite/scripts/scheduled_integration_test/deepseek_v2_lite_ep_eplb.sh:SC2086
+.buildkite/scripts/scheduled_integration_test/qwen30b_a3b_fp8_block_ep_eplb.sh:SC2086
+.buildkite/scripts/scheduled_integration_test/qwen3_next_mtp_async_eplb.sh:SC2086
+.buildkite/scripts/tpu/docker_run_bm.sh:SC1090
+.buildkite/scripts/tpu/docker_run_bm.sh:SC2086
+.buildkite/scripts/tpu/run_bm.sh:SC2034
+.buildkite/scripts/tpu/run_bm.sh:SC2086
+.buildkite/scripts/upload-nightly-wheels.sh:SC2086
+.buildkite/scripts/upload-nightly-wheels.sh:SC2115
+.buildkite/scripts/upload-nightly-wheels.sh:SC2236
+.buildkite/scripts/upload-release-wheels-pypi.sh:SC2086
+.buildkite/scripts/upload-rocm-wheels.sh:SC2012
+examples/online_serving/disaggregated_encoder/disagg_1e1p1d_example.sh:SC2086
+examples/online_serving/disaggregated_encoder/disagg_1e1pd_example.sh:SC2086
+examples/online_serving/disaggregated_prefill.sh:SC2086
+examples/online_serving/disaggregated_serving/kv_events.sh:SC2086
+examples/online_serving/disaggregated_serving/mooncake_connector/run_mooncake_connector.sh:SC2046
+examples/online_serving/disaggregated_serving/mooncake_connector/run_mooncake_connector.sh:SC2086
+examples/online_serving/disaggregated_serving/mooncake_connector/run_mooncake_connector.sh:SC2317
+examples/online_serving/disaggregated_serving_p2p_nccl_xpyd/disagg_example_p2p_nccl_xpyd.sh:SC2046
+examples/online_serving/disaggregated_serving_p2p_nccl_xpyd/disagg_example_p2p_nccl_xpyd.sh:SC2086
+examples/online_serving/disaggregated_serving_p2p_nccl_xpyd/disagg_example_p2p_nccl_xpyd.sh:SC2317
+examples/online_serving/elastic_ep/bench.sh:SC2086
+examples/online_serving/elastic_ep/serve_deepseek_v2.sh:SC2086
+examples/online_serving/multi-node-serving.sh:SC2006
+examples/online_serving/multi-node-serving.sh:SC2086
+examples/online_serving/multi-node-serving.sh:SC2181
+examples/others/lmcache/disagg_prefill_lmcache_v1/disagg_example_nixl.sh:SC2046
+examples/others/lmcache/disagg_prefill_lmcache_v1/disagg_example_nixl.sh:SC2126
+examples/others/lmcache/disagg_prefill_lmcache_v1/disagg_example_nixl.sh:SC2181
+examples/others/lmcache/disagg_prefill_lmcache_v1/disagg_example_nixl.sh:SC2206
+examples/others/lmcache/disagg_prefill_lmcache_v1/disagg_vllm_launcher.sh:SC2086
+examples/pooling/embed/openai_embedding_long_text/service.sh:SC2086
+tests/standalone_tests/python_only_compile.sh:SC2086
+tests/v1/ec_connector/integration/run_epd_correctness_test.sh:SC2086
+tests/v1/kv_connector/nixl_integration/config_sweep_accuracy_test.sh:SC2086
+tests/v1/kv_connector/nixl_integration/run_accuracy_test.sh:SC2005
+tests/v1/kv_connector/nixl_integration/run_accuracy_test.sh:SC2086
+tests/v1/kv_connector/nixl_integration/run_accuracy_test.sh:SC2124
+tests/v1/kv_connector/nixl_integration/run_accuracy_test.sh:SC2126
+tests/v1/kv_connector/nixl_integration/run_accuracy_test.sh:SC2206
+tests/v1/kv_connector/nixl_integration/run_edge_case_test.sh:SC2086
+tests/v1/kv_connector/nixl_integration/run_edge_case_test.sh:SC2153
+tests/v1/kv_connector/nixl_integration/run_tpu_disagg_accuracy_test.sh:SC2086
+tests/v1/kv_connector/nixl_integration/run_tpu_disagg_accuracy_test.sh:SC2089
+tests/v1/kv_connector/nixl_integration/run_tpu_disagg_accuracy_test.sh:SC2090
+tests/v1/kv_connector/nixl_integration/run_tpu_edge_case_test.sh:SC2086
+tests/v1/kv_connector/nixl_integration/run_tpu_edge_case_test.sh:SC2089
+tests/v1/kv_connector/nixl_integration/run_tpu_edge_case_test.sh:SC2090
+tools/ep_kernels/elastic_ep/install_eep_libraries.sh:SC2086
+tools/ep_kernels/install_python_libraries.sh:SC2086
+tools/ep_kernels/install_python_libraries.sh:SC2196
+tools/flashinfer-build.sh:SC2086
+tools/flashinfer-build.sh:SC2269
+tools/install_deepgemm.sh:SC2035
+tools/install_deepgemm.sh:SC2295
+tools/pre_commit/shellcheck.sh:SC2016
+tools/vllm-rocm/generate-rocm-wheels-root-index.sh:SC2295
+tools/vllm-tpu/build.sh:SC2145
diff --git a/tools/pre_commit/shellcheck.sh b/tools/pre_commit/shellcheck.sh
index 59ce40038..4adee5d57 100755
--- a/tools/pre_commit/shellcheck.sh
+++ b/tools/pre_commit/shellcheck.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
-set -e
+set -euo pipefail
 
 scversion="stable"
+baseline="tools/pre_commit/shellcheck.baseline"
 
 if [ -d "shellcheck-${scversion}" ]; then
     export PATH="$PATH:$(pwd)/shellcheck-${scversion}"
@@ -19,4 +20,38 @@ if ! [ -x "$(command -v shellcheck)" ]; then
 fi
 
 # TODO - fix warnings in .buildkite/scripts/hardware_ci/run-amd-test.sh
-find . -name "*.sh" ".git" -prune -not -path "./.buildkite/scripts/hardware_ci/run-amd-test.sh" -print0 | xargs -0 -I {} sh -c 'git check-ignore -q "{}" || shellcheck -s bash "{}"'
+# collects warnings as "file:SCcode" pairs for baseline comparison.
+collect() {
+  find . -path ./.git -prune -o -name "*.sh" \
+    -not -path "./.buildkite/scripts/hardware_ci/run-amd-test.sh" -print0 | \
+    xargs -0 sh -c 'for f in "$@"; do git check-ignore -q "$f" || shellcheck -s bash -f gcc "$f" || true; done' -- | \
+    sed -nE 's|^\./||; s|^([^:]+):[0-9]+:[0-9]+:.*\[(SC[0-9]+)\]$|\1:\2|p' | \
+    sort -u
+}
+
+if [[ "${1:-}" == "--generate-baseline" ]]; then
+  collect > "$baseline"
+  echo "Wrote baseline to $baseline"
+  exit 0
+fi
+
+if [[ ! -f "$baseline" ]]; then
+  echo "Baseline not found: $baseline (run: $0 --generate-baseline)"
+  exit 1
+fi
+
+current="$(mktemp)"
+trap 'rm -f "$current"' EXIT
+collect > "$current"
+
+# finds new warnings not in baseline
+new_errors="$(comm -23 "$current" <(sort -u "$baseline") || true)"
+if [ -n "$new_errors" ]; then
+  echo "$new_errors" | cut -d: -f1 | sort -u | while IFS= read -r file; do
+    if [[ -f "$file" ]]; then
+      codes=$(echo "$new_errors" | awk -F: -v f="$file" '$1==f {print $2}' | paste -sd ',' -)
+      shellcheck -s bash --include="$codes" "$file" 2>&1 || true
+    fi
+  done
+  exit 1
+fi