diff --git a/backend/packages/harness/deerflow/tools/builtins/task_tool.py b/backend/packages/harness/deerflow/tools/builtins/task_tool.py
index cf9281ff4..a45bff787 100644
--- a/backend/packages/harness/deerflow/tools/builtins/task_tool.py
+++ b/backend/packages/harness/deerflow/tools/builtins/task_tool.py
@@ -383,9 +383,6 @@ async def task_tool(
             # Polling timeout as a safety net (in case thread pool timeout doesn't work)
             # Set to execution timeout + 60s buffer, in 5s poll intervals
             # This catches edge cases where the background task gets stuck
-            # Note: We don't call cleanup_background_task here because the task may
-            # still be running in the background. The cleanup will happen when the
-            # executor completes and sets a terminal status.
             if poll_count > max_poll_count:
                 timeout_minutes = config.timeout_seconds // 60
                 logger.error(f"[trace={trace_id}] Task {task_id} polling timed out after {poll_count} polls (should have been caught by thread pool timeout)")
@@ -393,6 +390,11 @@ async def task_tool(
                 usage = _summarize_usage(getattr(result, "token_usage_records", None))
                 _cache_subagent_usage(tool_call_id, usage, enabled=cache_token_usage)
                 writer({"type": "task_timed_out", "task_id": task_id, "usage": usage})
+                # The task may still be running in the background. Signal cooperative
+                # cancellation and schedule deferred cleanup to remove the entry from
+                # _background_tasks once the background thread reaches a terminal state.
+                request_cancel_background_task(task_id)
+                _schedule_deferred_subagent_cleanup(task_id, trace_id, max_poll_count)
                 return f"Task polling timed out after {timeout_minutes} minutes. This may indicate the background task is stuck. Status: {result.status.value}"
     except asyncio.CancelledError:
         # Signal the background subagent thread to stop cooperatively.
diff --git a/backend/tests/test_task_tool_core_logic.py b/backend/tests/test_task_tool_core_logic.py
index 658968d65..dc0f844d3 100644
--- a/backend/tests/test_task_tool_core_logic.py
+++ b/backend/tests/test_task_tool_core_logic.py
@@ -732,17 +732,27 @@ def test_cleanup_called_on_timed_out(monkeypatch):
 
 
 def test_cleanup_not_called_on_polling_safety_timeout(monkeypatch):
-    """Verify cleanup_background_task is NOT called on polling safety timeout.
+    """Verify cleanup_background_task is NOT called directly on polling safety timeout.
 
-    This prevents race conditions where the background task is still running
-    but the polling loop gives up. The cleanup should happen later when the
-    executor completes and sets a terminal status.
+    The task is still RUNNING so it cannot be safely removed yet. Instead,
+    cooperative cancellation is requested and a deferred cleanup is scheduled.
     """
     config = _make_subagent_config()
     # Keep max_poll_count small for test speed: (1 + 60) // 5 = 12
     config.timeout_seconds = 1
     events = []
     cleanup_calls = []
+    cancel_requests = []
+    scheduled_cleanups = []
+
+    class DummyCleanupTask:
+        def add_done_callback(self, _callback):
+            return None
+
+    def fake_create_task(coro):
+        scheduled_cleanups.append(coro)
+        coro.close()
+        return DummyCleanupTask()
 
     monkeypatch.setattr(task_tool_module, "SubagentStatus", FakeSubagentStatus)
     monkeypatch.setattr(
@@ -759,12 +769,18 @@ def test_cleanup_not_called_on_polling_safety_timeout(monkeypatch):
     )
     monkeypatch.setattr(task_tool_module, "get_stream_writer", lambda: events.append)
     monkeypatch.setattr(task_tool_module.asyncio, "sleep", _no_sleep)
+    monkeypatch.setattr(task_tool_module.asyncio, "create_task", fake_create_task)
     monkeypatch.setattr("deerflow.tools.get_available_tools", lambda **kwargs: [])
     monkeypatch.setattr(
         task_tool_module,
         "cleanup_background_task",
         lambda task_id: cleanup_calls.append(task_id),
     )
+    monkeypatch.setattr(
+        task_tool_module,
+        "request_cancel_background_task",
+        lambda task_id: cancel_requests.append(task_id),
+    )
 
     output = _run_task_tool(
         runtime=_make_runtime(),
@@ -775,8 +791,12 @@ def test_cleanup_not_called_on_polling_safety_timeout(monkeypatch):
     )
 
     assert output.startswith("Task polling timed out after 0 minutes")
-    # cleanup should NOT be called because the task is still RUNNING
+    # cleanup_background_task must NOT be called directly (task is still RUNNING)
     assert cleanup_calls == []
+    # cooperative cancellation must be requested
+    assert cancel_requests == ["tc-no-cleanup-safety-timeout"]
+    # a deferred cleanup coroutine must be scheduled
+    assert len(scheduled_cleanups) == 1
 
 
 def test_cleanup_scheduled_on_cancellation(monkeypatch):