diff --git a/actions/setup/js/github_rate_limit_logger.cjs b/actions/setup/js/github_rate_limit_logger.cjs
index 1ddd7d717c1..4959c4a4c17 100644
--- a/actions/setup/js/github_rate_limit_logger.cjs
+++ b/actions/setup/js/github_rate_limit_logger.cjs
@@ -183,11 +183,23 @@ function createRateLimitAwareGithub(github) {
       get(target, method) {
         const fn = target[method];
         if (typeof fn !== "function") return fn;
-        return async (/** @type {any[]} */ ...args) => {
+        const wrapper = async (/** @type {any[]} */ ...args) => {
           const response = await fn.apply(target, args);
           logRateLimitFromResponse(response, `${namespaceName}.${String(method)}`);
           return response;
         };
+        // Wrap the wrapper in a Proxy so that Octokit-specific property accesses
+        // (e.g. .endpoint, used by github.paginate()) fall back to the original fn.
+        // Without this, github.paginate(github.rest.checks.listForRef, ...) throws
+        // "route.endpoint is not a function" because the wrapper does not have
+        // the .endpoint decorator that Octokit endpoint methods carry.
+        return new Proxy(wrapper, {
+          get(wrapperTarget, prop) {
+            const own = Reflect.get(wrapperTarget, prop);
+            if (own !== undefined) return own;
+            return Reflect.get(fn, prop);
+          },
+        });
       },
     });
   }
diff --git a/actions/setup/js/github_rate_limit_logger.test.cjs b/actions/setup/js/github_rate_limit_logger.test.cjs
index 2f695c7124a..eea782cc148 100644
--- a/actions/setup/js/github_rate_limit_logger.test.cjs
+++ b/actions/setup/js/github_rate_limit_logger.test.cjs
@@ -354,4 +354,49 @@ describe("createRateLimitAwareGithub", () => {
     expect(first.remaining).toBe(4999);
     expect(second.remaining).toBe(4998);
   });
+
+  it("preserves .endpoint on the wrapped method for github.paginate() compatibility", () => {
+    // Octokit endpoint-decorated methods (e.g. github.rest.checks.listForRef) carry
+    // a .endpoint property used by github.paginate() internally.  The proxy must
+    // forward .endpoint to the original function so paginate() doesn't throw
+    // "route.endpoint is not a function".
+    const endpointObj = { merge: vi.fn(), defaults: vi.fn() };
+    const mockListForRef = vi.fn().mockResolvedValue({ data: [], headers: {} });
+    mockListForRef.endpoint = endpointObj;
+
+    const mockGithub = {
+      rest: {
+        checks: { listForRef: mockListForRef },
+      },
+    };
+
+    const gh = createRateLimitAwareGithub(mockGithub);
+    const wrapped = gh.rest.checks.listForRef;
+
+    // The wrapped function must expose .endpoint from the original
+    expect(typeof wrapped).toBe("function");
+    expect(wrapped.endpoint).toBe(endpointObj);
+    expect(wrapped.endpoint.merge).toBe(endpointObj.merge);
+  });
+
+  it("allows github.paginate() to call endpoint.merge on the wrapped method", () => {
+    // Simulate how @octokit/plugin-paginate-rest v9+ uses the endpoint method:
+    //   const options = route.endpoint.merge(parameters)
+    const mergedOptions = { url: "/repos/o/r/commits/main/check-runs", per_page: 100 };
+    const endpointObj = { merge: vi.fn().mockReturnValue(mergedOptions) };
+    const mockListForRef = vi.fn().mockResolvedValue({ data: [], headers: {} });
+    mockListForRef.endpoint = endpointObj;
+
+    const mockGithub = {
+      rest: { checks: { listForRef: mockListForRef } },
+    };
+
+    const gh = createRateLimitAwareGithub(mockGithub);
+    const wrapped = gh.rest.checks.listForRef;
+
+    // paginate() would call this internally
+    const result = wrapped.endpoint.merge({ owner: "o", repo: "r", ref: "main", per_page: 100 });
+    expect(result).toBe(mergedOptions);
+    expect(endpointObj.merge).toHaveBeenCalledWith({ owner: "o", repo: "r", ref: "main", per_page: 100 });
+  });
 });
diff --git a/actions/setup/setup.sh b/actions/setup/setup.sh
index 50c0c80f3f0..4f3f823f19c 100755
--- a/actions/setup/setup.sh
+++ b/actions/setup/setup.sh
@@ -216,6 +216,7 @@ MCP_SCRIPTS_FILES=(
   "read_buffer.cjs"
   "generate_mcp_scripts_config.cjs"
   "setup_globals.cjs"
+  "github_rate_limit_logger.cjs"
   "error_helpers.cjs"
   "error_codes.cjs"
   "constants.cjs"
@@ -288,6 +289,7 @@ SAFE_OUTPUTS_FILES=(
   "write_large_content_to_file.cjs"
   "generate_compact_schema.cjs"
   "setup_globals.cjs"
+  "github_rate_limit_logger.cjs"
   "error_helpers.cjs"
   "error_codes.cjs"
   "constants.cjs"