diff --git a/qa/L2_jax_unittest/test.sh b/qa/L2_jax_unittest/test.sh
index 8441486e2c..38cbc8ad3d 100644
--- a/qa/L2_jax_unittest/test.sh
+++ b/qa/L2_jax_unittest/test.sh
@@ -31,11 +31,15 @@ mkdir -p "$XML_LOG_DIR"
 NVTE_JAX_UNITTEST_LEVEL="L2" python3 -m pytest -c $TE_PATH/tests/jax/pytest.ini -v --junitxml=$XML_LOG_DIR/pytest_jax_not_distributed.xml $TE_PATH/tests/jax -k 'not distributed' || test_fail "tests/jax/*not_distributed_*"
 
 pip3 install -r $TE_PATH/examples/jax/mnist/requirements.txt || error_exit "Failed to install mnist requirements"
-# Make mnist and encoder tests run-to-run deterministic for stable CI results
-export XLA_FLAGS="${XLA_FLAGS} --xla_gpu_deterministic_ops"
+# Note: mnist intentionally does NOT set --xla_gpu_deterministic_ops because it
+# significantly slows down small conv/GEMM kernels and was causing CI timeouts.
+# The mnist verify() already uses a tail-window min/max with relaxed thresholds
+# to be robust to run-to-run numerical noise.
 NVTE_JAX_UNITTEST_LEVEL="L2" python3 -m pytest -c $TE_PATH/tests/jax/pytest.ini -v --junitxml=$XML_LOG_DIR/pytest_mnist.xml $TE_PATH/examples/jax/mnist || test_fail "mnist"
 
 pip3 install -r $TE_PATH/examples/jax/encoder/requirements.txt || error_exit "Failed to install encoder requirements"
+# Make encoder tests to have run-to-run deterministic to have the stable CI results
+export XLA_FLAGS="${XLA_FLAGS} --xla_gpu_deterministic_ops"
 NVTE_JAX_UNITTEST_LEVEL="L2" python3 -m pytest -c $TE_PATH/tests/jax/pytest.ini -v --junitxml=$XML_LOG_DIR/pytest_test_single_gpu_encoder.xml $TE_PATH/examples/jax/encoder/test_single_gpu_encoder.py || test_fail "test_single_gpu_encoder.py"
 # Test without custom calls
 export XLA_FLAGS="${XLA_FLAGS} --xla_gpu_deterministic_ops"