diff --git a/packages/router-generator/src/generator.ts b/packages/router-generator/src/generator.ts
index 3ec4b46576a..0ecb325ceee 100644
--- a/packages/router-generator/src/generator.ts
+++ b/packages/router-generator/src/generator.ts
@@ -1357,7 +1357,24 @@ ${acc.routeTree.map((child) => `${child.variableName}Route: typeof ${getResolved
     prefixMap: RoutePrefixMap,
     config?: Config,
   ) {
-    const parentRoute = hasParentRoute(prefixMap, node, node.routePath)
+    let parentRoute = hasParentRoute(prefixMap, node, node.routePath)
+
+    // Fallback: check acc.routeNodesByPath for parents not in prefixMap
+    // This handles virtual routes created from lazy-only files that weren't
+    // in the initial prefixMap build
+    if (!parentRoute && node.routePath) {
+      let searchPath = node.routePath
+      while (searchPath.length > 0) {
+        const lastSlash = searchPath.lastIndexOf('/')
+        if (lastSlash <= 0) break
+        searchPath = searchPath.substring(0, lastSlash)
+        const candidate = acc.routeNodesByPath.get(searchPath)
+        if (candidate && candidate.routePath !== node.routePath) {
+          parentRoute = candidate
+          break
+        }
+      }
+    }
 
     if (parentRoute) node.parent = parentRoute
 
@@ -1489,7 +1506,11 @@ ${acc.routeTree.map((child) => `${child.variableName}Route: typeof ${getResolved
     }
 
     acc.routeNodes.push(node)
-    if (node.routePath && !node.isVirtual) {
+    if (node.routePath) {
+      // Always register routes by path so child routes can find parents.
+      // Virtual routes (created from lazy-only files) also need to be registered
+      // so that index routes like path.index.lazy.tsx can find their parent path.lazy.tsx.
+      // If a non-virtual route is later processed for the same path, it will overwrite.
       acc.routeNodesByPath.set(node.routePath, node)
     }
   }
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index/routeTree.snapshot.ts b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routeTree.snapshot.ts
new file mode 100644
index 00000000000..dd385cf7ac4
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routeTree.snapshot.ts
@@ -0,0 +1,89 @@
+/* eslint-disable */
+
+// @ts-nocheck
+
+// noinspection JSUnusedGlobalSymbols
+
+// This file was automatically generated by TanStack Router.
+// You should NOT make any changes in this file as it will be overwritten.
+// Additionally, you should also exclude this file from your linter and/or formatter to prevent it from being checked or modified.
+
+import { createFileRoute } from '@tanstack/react-router'
+
+import { Route as rootRouteImport } from './routes/__root'
+
+const PathLazyRouteImport = createFileRoute('/path')()
+const PathIndexLazyRouteImport = createFileRoute('/path/')()
+
+const PathLazyRoute = PathLazyRouteImport.update({
+  id: '/path',
+  path: '/path',
+  getParentRoute: () => rootRouteImport,
+} as any).lazy(() => import('./routes/path.lazy').then((d) => d.Route))
+const PathIndexLazyRoute = PathIndexLazyRouteImport.update({
+  id: '/',
+  path: '/',
+  getParentRoute: () => PathLazyRoute,
+} as any).lazy(() => import('./routes/path.index.lazy').then((d) => d.Route))
+
+export interface FileRoutesByFullPath {
+  '/path': typeof PathLazyRouteWithChildren
+  '/path/': typeof PathIndexLazyRoute
+}
+export interface FileRoutesByTo {
+  '/path': typeof PathIndexLazyRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/path': typeof PathLazyRouteWithChildren
+  '/path/': typeof PathIndexLazyRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/path' | '/path/'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/path'
+  id: '__root__' | '/path' | '/path/'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  PathLazyRoute: typeof PathLazyRouteWithChildren
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/path': {
+      id: '/path'
+      path: '/path'
+      fullPath: '/path'
+      preLoaderRoute: typeof PathLazyRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/path/': {
+      id: '/path/'
+      path: '/'
+      fullPath: '/path/'
+      preLoaderRoute: typeof PathIndexLazyRouteImport
+      parentRoute: typeof PathLazyRoute
+    }
+  }
+}
+
+interface PathLazyRouteChildren {
+  PathIndexLazyRoute: typeof PathIndexLazyRoute
+}
+
+const PathLazyRouteChildren: PathLazyRouteChildren = {
+  PathIndexLazyRoute: PathIndexLazyRoute,
+}
+
+const PathLazyRouteWithChildren = PathLazyRoute._addFileChildren(
+  PathLazyRouteChildren,
+)
+
+const rootRouteChildren: RootRouteChildren = {
+  PathLazyRoute: PathLazyRouteWithChildren,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/__root.tsx b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/__root.tsx
new file mode 100644
index 00000000000..87099187f86
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/__root.tsx
@@ -0,0 +1,2 @@
+import { createRootRoute } from '@tanstack/react-router'
+export const Route = createRootRoute()
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/path.index.lazy.tsx b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/path.index.lazy.tsx
new file mode 100644
index 00000000000..2710d8adab8
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/path.index.lazy.tsx
@@ -0,0 +1,4 @@
+import { createLazyFileRoute } from '@tanstack/react-router'
+export const Route = createLazyFileRoute('/path/')({
+  component: () => 'Path Index',
+})
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/path.lazy.tsx b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/path.lazy.tsx
new file mode 100644
index 00000000000..1b707b69948
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index/routes/path.lazy.tsx
@@ -0,0 +1,4 @@
+import { createLazyFileRoute } from '@tanstack/react-router'
+export const Route = createLazyFileRoute('/path')({
+  component: () => 'Path Layout',
+})