diff --git a/tests/entrypoints/openai/test_response_api_with_harmony.py b/tests/entrypoints/openai/test_response_api_with_harmony.py
index b882a2f9326e2..400779064ef51 100644
--- a/tests/entrypoints/openai/test_response_api_with_harmony.py
+++ b/tests/entrypoints/openai/test_response_api_with_harmony.py
@@ -698,6 +698,22 @@ async def test_function_calling_required(client: OpenAI, model_name: str):
         )
 
 
+@pytest.mark.asyncio
+@pytest.mark.parametrize("model_name", [MODEL_NAME])
+async def test_system_message_with_tools(client: OpenAI, model_name: str):
+    from vllm.entrypoints.harmony_utils import get_system_message
+
+    # Test with custom tools enabled - commentary channel should be available
+    sys_msg = get_system_message(with_custom_tools=True)
+    valid_channels = sys_msg.content[0].channel_config.valid_channels
+    assert "commentary" in valid_channels
+
+    # Test with custom tools disabled - commentary channel should be removed
+    sys_msg = get_system_message(with_custom_tools=False)
+    valid_channels = sys_msg.content[0].channel_config.valid_channels
+    assert "commentary" not in valid_channels
+
+
 @pytest.mark.asyncio
 @pytest.mark.parametrize("model_name", [MODEL_NAME])
 async def test_function_calling_full_history(client: OpenAI, model_name: str):
diff --git a/vllm/entrypoints/openai/serving_chat.py b/vllm/entrypoints/openai/serving_chat.py
index ab4bf75102f43..2336158ac51ba 100644
--- a/vllm/entrypoints/openai/serving_chat.py
+++ b/vllm/entrypoints/openai/serving_chat.py
@@ -1575,7 +1575,9 @@ class OpenAIServingChat(OpenAIServing):
         sys_msg = get_system_message(
             reasoning_effort=request.reasoning_effort,
             browser_description=None,
-            python_description=None)
+            python_description=None,
+            with_custom_tools=request.tools is not None
+            )
         messages.append(sys_msg)
 
         # Add developer message.