diff --git a/.github/workflows/scripts/run_ci_command.py b/.github/workflows/scripts/run_ci_command.py
index b6ef1c3ae8..142249476d 100644
--- a/.github/workflows/scripts/run_ci_command.py
+++ b/.github/workflows/scripts/run_ci_command.py
@@ -861,14 +861,24 @@ def merge_base_into_pr(
         for _ in range(BRANCH_UPDATE_POLL_ATTEMPTS):
             time.sleep(BRANCH_UPDATE_POLL_SECONDS)
             current_pr = github.get_pr(pr["number"])
-            if current_pr["head"]["sha"] != pr["head"]["sha"]:
-                break
+            if current_pr["head"]["sha"] == pr["head"]["sha"]:
+                continue
+            try:
+                behind = github.get_commits_behind_base(
+                    base_ref, current_pr["head"]["sha"]
+                )
+            except ApiError as error:
+                # A fork's new head is briefly unknown to the base repository.
+                if error.status == 404:
+                    continue
+                raise
+            break
         else:
             raise merge_failed("the merge commit did not appear in time")
         if (
             current_pr["state"] != "open"
             or current_pr["base"]["ref"] != base_ref
-            or github.get_commits_behind_base(base_ref, current_pr["head"]["sha"])
+            or behind
         ):
             raise merge_failed("the PR changed during the merge")
     except ApiError as error:
diff --git a/.github/workflows/scripts/test_run_ci_command.py b/.github/workflows/scripts/test_run_ci_command.py
index 2061ff895e..220af20e8b 100644
--- a/.github/workflows/scripts/test_run_ci_command.py
+++ b/.github/workflows/scripts/test_run_ci_command.py
@@ -677,6 +677,24 @@ class RunCiCommandTest(unittest.TestCase):
                     self.assertIn("CI already ran on this commit", github.comments[0])
                     self.assertIn("`/ci retry`", github.comments[0])
 
+    def test_run_waits_for_fork_merge_commit_to_reach_base_repo(self) -> None:
+        github = FakeGitHub(behind=5)
+        updater = FakeBranchUpdater(github)
+        buildkite = FakeBuildkite([[], []])
+
+        with (
+            patch("run_ci_command.time.sleep"),
+            patch.object(
+                github,
+                "get_commits_behind_base",
+                side_effect=[5, ApiError(404, "Not Found"), 0],
+            ),
+        ):
+            run(make_event(COMMAND_RUN_CI), github, buildkite, "", updater)
+
+        self.assertEqual(buildkite.created_builds[0]["commit"], "merge-commit-sha")
+        self.assertTrue(github.comments[0].startswith("✅ "))
+
     def test_run_reports_failed_merge_without_building(self) -> None:
         github = FakeGitHub(behind=5)
         updater = FakeBranchUpdater(github, error=ApiError(422, "merge conflict"))