diff --git a/.changeset/red-pugs-itch.md b/.changeset/red-pugs-itch.md
new file mode 100644
index 0000000000..39fd463d92
--- /dev/null
+++ b/.changeset/red-pugs-itch.md
@@ -0,0 +1,5 @@
+---
+"@react-router/fs-routes": patch
+---
+
+Resolve route file outside of app directory relative to app directory
diff --git a/packages/react-router-fs-routes/__tests__/flatRoutes-test.ts b/packages/react-router-fs-routes/__tests__/flatRoutes-test.ts
index 5e7b2e8e1d..4ce23adc02 100644
--- a/packages/react-router-fs-routes/__tests__/flatRoutes-test.ts
+++ b/packages/react-router-fs-routes/__tests__/flatRoutes-test.ts
@@ -912,4 +912,27 @@ describe("flatRoutes", () => {
       );
     });
   });
+
+  describe("generates route manifest entry files relative to the app directory", () => {
+    let testCases: [string, string][] = [
+      [path.posix.join(APP_DIR, "routes"), "routes"],
+      [
+        path.posix.join(APP_DIR, "..", "routes"),
+        path.posix.join("..", "routes"),
+      ],
+    ];
+
+    let fileName = "route.tsx";
+
+    testCases.forEach(([routesDir, expected]) => {
+      test(`for routes directory "${routesDir}"`, () => {
+        let routeFile = path.posix.join(routesDir, fileName);
+        let routeInfo = flatRoutesUniversal(APP_DIR, [routeFile]);
+        let routes = Object.values(routeInfo);
+
+        expect(routes).toHaveLength(1);
+        expect(routes[0].file).toBe(path.posix.join(expected, fileName));
+      });
+    });
+  });
 });
diff --git a/packages/react-router-fs-routes/flatRoutes.ts b/packages/react-router-fs-routes/flatRoutes.ts
index 63265f84d1..49c015bf39 100644
--- a/packages/react-router-fs-routes/flatRoutes.ts
+++ b/packages/react-router-fs-routes/flatRoutes.ts
@@ -134,6 +134,8 @@ export function flatRoutesUniversal(
   let prefixLookup = new PrefixLookupTrie();
   let uniqueRoutes = new Map<string, RouteManifestEntry>();
   let routeIdConflicts = new Map<string, string[]>();
+  let normalizedApp = normalizeSlashes(appDirectory);
+  let appWithPrefix = path.posix.join(normalizedApp, prefix);
 
   // id -> file
   let routeIds = new Map<string, string>();
@@ -142,9 +144,8 @@ export function flatRoutesUniversal(
     let normalizedFile = normalizeSlashes(file);
     let routeExt = path.extname(normalizedFile);
     let routeDir = path.dirname(normalizedFile);
-    let normalizedApp = normalizeSlashes(appDirectory);
     let routeId =
-      routeDir === path.posix.join(normalizedApp, prefix)
+      routeDir === appWithPrefix
         ? path.posix
             .relative(normalizedApp, normalizedFile)
             .slice(0, -routeExt.length)
@@ -174,7 +175,7 @@ export function flatRoutesUniversal(
     let pathname = createRoutePath(segments, raw, index);
 
     routeManifest[routeId] = {
-      file: file.slice(appDirectory.length + 1),
+      file: path.posix.relative(normalizedApp, file),
       id: routeId,
       path: pathname,
     };