diff --git a/airflow-core/src/airflow/api_fastapi/execution_api/routes/task_instances.py b/airflow-core/src/airflow/api_fastapi/execution_api/routes/task_instances.py
index 9273cc8b3d487..5aaf0e2ef56bf 100644
--- a/airflow-core/src/airflow/api_fastapi/execution_api/routes/task_instances.py
+++ b/airflow-core/src/airflow/api_fastapi/execution_api/routes/task_instances.py
@@ -545,9 +545,27 @@ def ti_skip_downstream(
     task_ids = [task if isinstance(task, tuple) else (task, -1) for task in tasks]
     log.debug("Prepared task IDs for skipping", task_ids=task_ids)
 
+    # Don't overwrite tasks that are already executing or finished.
+    # See: https://github.com/apache/airflow/issues/59378
+    # Note: SQL NULL NOT IN (...) is falsy, so we need an explicit IS NULL check.
+    skippable_state_clause = or_(
+        TI.state.is_(None),
+        TI.state.not_in(
+            [
+                TaskInstanceState.RUNNING,
+                TaskInstanceState.SUCCESS,
+                TaskInstanceState.FAILED,
+            ]
+        ),
+    )
     query = (
         update(TI)
-        .where(TI.dag_id == dag_id, TI.run_id == run_id, tuple_(TI.task_id, TI.map_index).in_(task_ids))
+        .where(
+            TI.dag_id == dag_id,
+            TI.run_id == run_id,
+            tuple_(TI.task_id, TI.map_index).in_(task_ids),
+            skippable_state_clause,
+        )
         .values(state=TaskInstanceState.SKIPPED, start_date=now, end_date=now)
         .execution_options(synchronize_session=False)
     )
diff --git a/airflow-core/tests/unit/api_fastapi/execution_api/versions/head/test_task_instances.py b/airflow-core/tests/unit/api_fastapi/execution_api/versions/head/test_task_instances.py
index d9ec3916187ee..c064c399183a1 100644
--- a/airflow-core/tests/unit/api_fastapi/execution_api/versions/head/test_task_instances.py
+++ b/airflow-core/tests/unit/api_fastapi/execution_api/versions/head/test_task_instances.py
@@ -1481,6 +1481,95 @@ def test_ti_skip_downstream(self, client, session, create_task_instance, dag_mak
         assert ti1.state == State.SKIPPED
 
 
+class TestTISkipDownstreamRaceCondition:
+    """Regression tests for #59378: state guard in ti_skip_downstream()."""
+
+    def setup_method(self):
+        clear_db_runs()
+
+    def teardown_method(self):
+        clear_db_runs()
+
+    @pytest.mark.parametrize(
+        "initial_state",
+        [
+            State.RUNNING,
+            State.SUCCESS,
+            State.FAILED,
+        ],
+    )
+    def test_skip_downstream_does_not_overwrite_terminal_or_running_ti(
+        self, client, session, dag_maker, initial_state
+    ):
+        with dag_maker(f"skip_race_dag_{initial_state}", session=session):
+            branch = EmptyOperator(task_id="branch")
+            downstream = EmptyOperator(task_id="downstream")
+            branch >> downstream
+        dr = dag_maker.create_dagrun(run_id="run")
+
+        ti_branch = dr.get_task_instance("branch")
+        ti_branch.set_state(State.SUCCESS)
+
+        ti_downstream = dr.get_task_instance("downstream")
+        ti_downstream.set_state(initial_state)
+        session.commit()
+
+        response = client.patch(
+            f"/execution/task-instances/{ti_branch.id}/skip-downstream",
+            json={"tasks": ["downstream"]},
+        )
+        assert response.status_code == 204
+
+        session.expire_all()
+        ti_downstream = dr.get_task_instance("downstream")
+        assert ti_downstream.state == initial_state
+
+    def test_skip_downstream_does_skip_queued_ti(self, client, session, dag_maker):
+        with dag_maker("skip_race_dag_queued", session=session):
+            branch = EmptyOperator(task_id="branch")
+            downstream = EmptyOperator(task_id="downstream")
+            branch >> downstream
+        dr = dag_maker.create_dagrun(run_id="run")
+
+        ti_branch = dr.get_task_instance("branch")
+        ti_branch.set_state(State.SUCCESS)
+
+        ti_downstream = dr.get_task_instance("downstream")
+        ti_downstream.set_state(TaskInstanceState.QUEUED)
+        session.commit()
+
+        response = client.patch(
+            f"/execution/task-instances/{ti_branch.id}/skip-downstream",
+            json={"tasks": ["downstream"]},
+        )
+        assert response.status_code == 204
+
+        session.expire_all()
+        ti_downstream = dr.get_task_instance("downstream")
+        assert ti_downstream.state == State.SKIPPED
+
+    def test_skip_downstream_still_skips_none_state_ti(self, client, session, dag_maker):
+        with dag_maker("skip_race_dag_normal", session=session):
+            branch = EmptyOperator(task_id="branch")
+            downstream = EmptyOperator(task_id="downstream")
+            branch >> downstream
+        dr = dag_maker.create_dagrun(run_id="run")
+
+        ti_branch = dr.get_task_instance("branch")
+        ti_branch.set_state(State.SUCCESS)
+        session.commit()
+
+        response = client.patch(
+            f"/execution/task-instances/{ti_branch.id}/skip-downstream",
+            json={"tasks": ["downstream"]},
+        )
+        assert response.status_code == 204
+
+        session.expire_all()
+        ti_downstream = dr.get_task_instance("downstream")
+        assert ti_downstream.state == State.SKIPPED
+
+
 class TestTIHealthEndpoint:
     def setup_method(self):
         clear_db_runs()