diff --git a/src/prefect/runner/runner.py b/src/prefect/runner/runner.py
index 26a0ee01aafc..fa6c6e459996 100644
--- a/src/prefect/runner/runner.py
+++ b/src/prefect/runner/runner.py
@@ -798,7 +798,20 @@ def _acquire_limit_slot(self, flow_run_id: str) -> bool:
         try:
             if self._limiter:
                 self._limiter.acquire_on_behalf_of_nowait(flow_run_id)
+                self._logger.debug("Limit slot acquired for flow run '%s'", flow_run_id)
             return True
+        except RuntimeError as exc:
+            if (
+                "this borrower is already holding one of this CapacityLimiter's tokens"
+                in str(exc)
+            ):
+                self._logger.warning(
+                    f"Duplicate submission of flow run '{flow_run_id}' detected. Runner"
+                    " will not re-submit flow run."
+                )
+                return False
+            else:
+                raise
         except anyio.WouldBlock:
             self._logger.info(
                 f"Flow run limit reached; {self._limiter.borrowed_tokens} flow runs"
@@ -813,6 +826,7 @@ def _release_limit_slot(self, flow_run_id: str) -> None:
         """
         if self._limiter:
             self._limiter.release_on_behalf_of(flow_run_id)
+            self._logger.debug("Limit slot released for flow run '%s'", flow_run_id)
 
     async def _submit_scheduled_flow_runs(
         self, flow_run_response: List["FlowRun"]
diff --git a/tests/runner/test_runner.py b/tests/runner/test_runner.py
index 0df76ff64abe..b77c08444d44 100644
--- a/tests/runner/test_runner.py
+++ b/tests/runner/test_runner.py
@@ -690,6 +690,37 @@ async def test_runner_caches_adhoc_pulls(self, prefect_client):
         # Should be 3 because the ad hoc pull should have been cached
         assert runner._storage_objs[0]._pull_code_spy.call_count == 3
 
+    @pytest.mark.usefixtures("use_hosted_api_server")
+    async def test_runner_does_not_raise_on_duplicate_submission(self, prefect_client):
+        """
+        Regression test for https://github.com/PrefectHQ/prefect/issues/11093
+
+        The runner has a race condition where it can try to borrow a limit slot
+        that it already has. This test ensures that the runner does not raise
+        an exception in this case.
+        """
+        async with Runner(pause_on_shutdown=False) as runner:
+            deployment = RunnerDeployment.from_flow(
+                flow=tired_flow,
+                name=__file__,
+            )
+
+            deployment_id = await runner.add_deployment(deployment)
+
+            flow_run = await prefect_client.create_flow_run_from_deployment(
+                deployment_id=deployment_id
+            )
+            # acquire the limit slot and then try to borrow it again
+            # during submission to simulate race condition
+            runner._acquire_limit_slot(flow_run.id)
+            await runner._get_and_submit_flow_runs()
+
+            # shut down cleanly
+            runner.started = False
+            runner.stopping = True
+            runner._cancelling_flow_run_ids.add(flow_run.id)
+            await runner._cancel_run(flow_run)
+
 
 class TestRunnerDeployment:
     @pytest.fixture