diff --git a/build_tools/github_actions/configure_external_repo_ci.py b/build_tools/github_actions/configure_external_repo_ci.py
index 9f2e9813b5e..fb787570978 100644
--- a/build_tools/github_actions/configure_external_repo_ci.py
+++ b/build_tools/github_actions/configure_external_repo_ci.py
@@ -55,6 +55,8 @@
     TypeVar,
 )
 
+from github_actions_api import gha_load_github_event
+
 logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s")
 logger = logging.getLogger(__name__)
 
@@ -194,6 +196,47 @@ def get_modified_paths_api(
     return {f["filename"] for f in files}
 
 
+@retry(
+    max_attempts=3,
+    delay_seconds=2,
+    exceptions=(subprocess.TimeoutExpired, subprocess.CalledProcessError),
+)
+def get_pr_modified_paths_api(github_repo: str, pr_number: int) -> Optional[Set[str]]:
+    """Get paths of files changed in a PR using GitHub API (PR files endpoint).
+
+    Returns None if the result is truncated (3000+ files).
+    """
+    result = subprocess.run(
+        [
+            "gh",
+            "api",
+            "--paginate",
+            f"repos/{github_repo}/pulls/{pr_number}/files?per_page=100",
+            "--jq",
+            ".[].filename",
+        ],
+        capture_output=True,
+        text=True,
+        check=True,
+        timeout=120,
+    )
+    files = result.stdout.splitlines()
+    # GitHub PR files API returns max 3000 files
+    if len(files) >= 3000:
+        logger.warning("PR files API returned 3000+ files, result may be truncated")
+        return None
+    return set(files)
+
+
+def get_event_pr_number() -> Optional[int]:
+    """Return the PR number from the GitHub Actions event payload, if any."""
+    try:
+        event = gha_load_github_event()
+    except KeyError:
+        return None
+    return event.get("pull_request", {}).get("number")
+
+
 def matches_patterns(paths: Iterable[str], patterns: Iterable[str]) -> bool:
     """Check if any path matches any pattern."""
     for path in paths:
@@ -329,6 +372,10 @@ def configure(
     if event_name == "pull_request" and base_sha and head_sha:
         logger.info(f"Getting PR diff via API: {base_sha}...{head_sha}")
         modified_paths = get_modified_paths_api(github_repo, base_sha, head_sha)
+        pr_number = get_event_pr_number() if modified_paths is None else None
+        if pr_number:
+            logger.info(f"Getting PR #{pr_number} files via API")
+            modified_paths = get_pr_modified_paths_api(github_repo, pr_number)
     elif event_name == "push" and base_sha and head_sha:
         # For push, the caller passes github.event.before as base_sha;
         # the compare API does not understand git "^" ancestry syntax.
diff --git a/build_tools/tests/configure_external_repo_ci_test.py b/build_tools/tests/configure_external_repo_ci_test.py
index 37b02d9604b..0053ef3f08e 100644
--- a/build_tools/tests/configure_external_repo_ci_test.py
+++ b/build_tools/tests/configure_external_repo_ci_test.py
@@ -272,8 +272,9 @@ def test_project_change_returns_changed_projects(self, mock_config, mock_api):
         self.assertEqual(result.changed_projects, "projects/rocblas")
         self.assertEqual(result.run_all_tests, False)
 
+    @patch("configure_external_repo_ci.get_event_pr_number", return_value=None)
     @patch("configure_external_repo_ci.get_modified_paths_api")
-    def test_truncated_api_response_runs_all_tests(self, mock_api):
+    def test_truncated_api_response_runs_all_tests(self, mock_api, _mock_pr_number):
         mock_api.return_value = None  # Signals truncated response
         result = configure(
             event_name="pull_request",
@@ -284,6 +285,28 @@ def test_truncated_api_response_runs_all_tests(self, mock_api):
         )
         self.assertEqual(result.run_all_tests, True)
 
+    @patch("configure_external_repo_ci.get_pr_modified_paths_api")
+    @patch("configure_external_repo_ci.get_event_pr_number", return_value=123)
+    @patch("configure_external_repo_ci.get_modified_paths_api", return_value=None)
+    @patch("configure_external_repo_ci.load_repo_config")
+    def test_truncated_compare_falls_back_to_pr_files(
+        self, mock_config, _mock_api, _mock_pr_number, mock_pr_files
+    ):
+        mock_pr_files.return_value = {"projects/rocblas/src/main.cpp"}
+        mock_config.return_value = [
+            RepoEntry(name="rocblas", url="", branch="", category="projects"),
+        ]
+        result = configure(
+            event_name="pull_request",
+            github_repo="ROCm/rocm-libraries",
+            base_sha="abc123",
+            head_sha="def456",
+            config_path=".github/repos-config.json",
+        )
+        mock_pr_files.assert_called_once_with("ROCm/rocm-libraries", 123)
+        self.assertEqual(result.changed_projects, "projects/rocblas")
+        self.assertEqual(result.run_all_tests, False)
+
     def test_no_shas_provided_runs_all_tests(self):
         result = configure(
             event_name="pull_request",