diff --git a/packages/router-generator/src/generator.ts b/packages/router-generator/src/generator.ts
index e7009eb8369..62cab9a106d 100644
--- a/packages/router-generator/src/generator.ts
+++ b/packages/router-generator/src/generator.ts
@@ -1422,19 +1422,33 @@ ${acc.routeTree.map((child) => `${child.variableName}Route: typeof ${getResolved
   ) {
     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) {
+    // Check routeNodesByPath for a closer parent that may not be in prefixMap.
+    //
+    // Why: The prefixMap excludes lazy routes by design. When lazy-only routes are
+    // nested inside a pathless layout, the virtual route created from the lazy file
+    // won't be in the prefixMap, but it will be in routeNodesByPath.
+    //
+    // Example: Given files _layout/path.lazy.tsx and _layout/path.index.lazy.tsx:
+    //   - prefixMap contains: /_layout (from route.tsx)
+    //   - routeNodesByPath contains: /_layout AND /_layout/path (virtual from lazy)
+    //   - For /_layout/path/, hasParentRoute returns /_layout (wrong)
+    //   - But the correct parent is /_layout/path (the virtual route from path.lazy.tsx)
+    //
+    // Optimization: Only search if we might find a closer parent. The search walks
+    // up from the immediate parent path, so if the first candidate matches what
+    // prefixMap found, there's no closer parent to find.
+    if (node.routePath) {
+      const lastSlash = node.routePath.lastIndexOf('/')
+      if (lastSlash > 0) {
+        const immediateParentPath = node.routePath.substring(0, lastSlash)
+        const candidate = acc.routeNodesByPath.get(immediateParentPath)
+        if (
+          candidate &&
+          candidate.routePath !== node.routePath &&
+          candidate !== parentRoute
+        ) {
+          // Found a closer parent in routeNodesByPath that differs from prefixMap result
           parentRoute = candidate
-          break
         }
       }
     }
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routeTree.snapshot.ts b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routeTree.snapshot.ts
new file mode 100644
index 00000000000..2de1aa6bb67
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routeTree.snapshot.ts
@@ -0,0 +1,118 @@
+/* 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'
+import { Route as LayoutRouteRouteImport } from './routes/_layout/route'
+
+const LayoutPathLazyRouteImport = createFileRoute('/_layout/path')()
+const LayoutPathIndexLazyRouteImport = createFileRoute('/_layout/path/')()
+
+const LayoutRouteRoute = LayoutRouteRouteImport.update({
+  id: '/_layout',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const LayoutPathLazyRoute = LayoutPathLazyRouteImport.update({
+  id: '/path',
+  path: '/path',
+  getParentRoute: () => LayoutRouteRoute,
+} as any).lazy(() => import('./routes/_layout/path.lazy').then((d) => d.Route))
+const LayoutPathIndexLazyRoute = LayoutPathIndexLazyRouteImport.update({
+  id: '/',
+  path: '/',
+  getParentRoute: () => LayoutPathLazyRoute,
+} as any).lazy(() =>
+  import('./routes/_layout/path.index.lazy').then((d) => d.Route),
+)
+
+export interface FileRoutesByFullPath {
+  '/': typeof LayoutRouteRouteWithChildren
+  '/path': typeof LayoutPathLazyRouteWithChildren
+  '/path/': typeof LayoutPathIndexLazyRoute
+}
+export interface FileRoutesByTo {
+  '/': typeof LayoutRouteRouteWithChildren
+  '/path': typeof LayoutPathIndexLazyRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/_layout': typeof LayoutRouteRouteWithChildren
+  '/_layout/path': typeof LayoutPathLazyRouteWithChildren
+  '/_layout/path/': typeof LayoutPathIndexLazyRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/' | '/path' | '/path/'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/' | '/path'
+  id: '__root__' | '/_layout' | '/_layout/path' | '/_layout/path/'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  LayoutRouteRoute: typeof LayoutRouteRouteWithChildren
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/_layout': {
+      id: '/_layout'
+      path: ''
+      fullPath: '/'
+      preLoaderRoute: typeof LayoutRouteRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/_layout/path': {
+      id: '/_layout/path'
+      path: '/path'
+      fullPath: '/path'
+      preLoaderRoute: typeof LayoutPathLazyRouteImport
+      parentRoute: typeof LayoutRouteRoute
+    }
+    '/_layout/path/': {
+      id: '/_layout/path/'
+      path: '/'
+      fullPath: '/path/'
+      preLoaderRoute: typeof LayoutPathIndexLazyRouteImport
+      parentRoute: typeof LayoutPathLazyRoute
+    }
+  }
+}
+
+interface LayoutPathLazyRouteChildren {
+  LayoutPathIndexLazyRoute: typeof LayoutPathIndexLazyRoute
+}
+
+const LayoutPathLazyRouteChildren: LayoutPathLazyRouteChildren = {
+  LayoutPathIndexLazyRoute: LayoutPathIndexLazyRoute,
+}
+
+const LayoutPathLazyRouteWithChildren = LayoutPathLazyRoute._addFileChildren(
+  LayoutPathLazyRouteChildren,
+)
+
+interface LayoutRouteRouteChildren {
+  LayoutPathLazyRoute: typeof LayoutPathLazyRouteWithChildren
+}
+
+const LayoutRouteRouteChildren: LayoutRouteRouteChildren = {
+  LayoutPathLazyRoute: LayoutPathLazyRouteWithChildren,
+}
+
+const LayoutRouteRouteWithChildren = LayoutRouteRoute._addFileChildren(
+  LayoutRouteRouteChildren,
+)
+
+const rootRouteChildren: RootRouteChildren = {
+  LayoutRouteRoute: LayoutRouteRouteWithChildren,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/__root.tsx b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/__root.tsx
new file mode 100644
index 00000000000..9c657c7d5b4
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/__root.tsx
@@ -0,0 +1,3 @@
+import { createRootRoute } from '@tanstack/react-router'
+
+export const Route = createRootRoute()
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/path.index.lazy.tsx b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/path.index.lazy.tsx
new file mode 100644
index 00000000000..86103a57963
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/path.index.lazy.tsx
@@ -0,0 +1,5 @@
+import { createLazyFileRoute } from '@tanstack/react-router'
+
+export const Route = createLazyFileRoute('/_layout/path/')({
+  component: () => 'Path Index',
+})
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/path.lazy.tsx b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/path.lazy.tsx
new file mode 100644
index 00000000000..8778295a8dd
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/path.lazy.tsx
@@ -0,0 +1,5 @@
+import { createLazyFileRoute } from '@tanstack/react-router'
+
+export const Route = createLazyFileRoute('/_layout/path')({
+  component: () => 'Path Layout',
+})
diff --git a/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/route.tsx b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/route.tsx
new file mode 100644
index 00000000000..da869f097e0
--- /dev/null
+++ b/packages/router-generator/tests/generator/lazy-only-layout-and-index-in-pathless/routes/_layout/route.tsx
@@ -0,0 +1,9 @@
+import { Outlet, createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout')({
+  component: RouteComponent,
+})
+
+function RouteComponent() {
+  return <Outlet />
+}