diff --git a/packages/router-generator/src/filesystem/physical/getRouteNodes.ts b/packages/router-generator/src/filesystem/physical/getRouteNodes.ts
index 0c64052f6c..de22b726ed 100644
--- a/packages/router-generator/src/filesystem/physical/getRouteNodes.ts
+++ b/packages/router-generator/src/filesystem/physical/getRouteNodes.ts
@@ -114,6 +114,10 @@ export async function getRouteNodes(
           `${dir}/${removeExt(node.filePath)}`,
         )
         node.routePath = routePath
+        // Keep originalRoutePath aligned with routePath for escape detection
+        if (node.originalRoutePath) {
+          node.originalRoutePath = `/${dir}${node.originalRoutePath}`
+        }
         node.filePath = filePath
       })
 
diff --git a/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts b/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts
index 35e35d85e6..920e066ab1 100644
--- a/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts
+++ b/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts
@@ -1,5 +1,6 @@
 import path, { join, resolve } from 'node:path'
 import {
+  determineInitialRoutePath,
   removeExt,
   removeLeadingSlash,
   removeTrailingSlash,
@@ -156,6 +157,10 @@ export async function getRouteNodesRecursive(
             `${node.pathPrefix}/${removeExt(subtreeNode.filePath)}`,
           )
           subtreeNode.routePath = `${parent?.routePath ?? ''}${node.pathPrefix}${subtreeNode.routePath}`
+          // Keep originalRoutePath aligned with routePath for escape detection
+          if (subtreeNode.originalRoutePath) {
+            subtreeNode.originalRoutePath = `${parent?.routePath ?? ''}${node.pathPrefix}${subtreeNode.originalRoutePath}`
+          }
           subtreeNode.filePath = `${node.directory}/${subtreeNode.filePath}`
         })
         return routeNodes
@@ -186,7 +191,15 @@ export async function getRouteNodesRecursive(
           const lastSegment = node.path
           let routeNode: RouteNode
 
-          const routePath = `${parentRoutePath}/${removeLeadingSlash(lastSegment)}`
+          // Process the segment to handle escape sequences like [_]
+          const {
+            routePath: escapedSegment,
+            originalRoutePath: originalSegment,
+          } = determineInitialRoutePath(removeLeadingSlash(lastSegment))
+          const routePath = `${parentRoutePath}${escapedSegment}`
+          // Store the original path with brackets for escape detection
+          const originalRoutePath = `${parentRoutePath}${originalSegment}`
+
           if (node.file) {
             const { filePath, variableName, fullPath } = getFile(node.file)
             routeNode = {
@@ -194,6 +207,7 @@ export async function getRouteNodesRecursive(
               fullPath,
               variableName,
               routePath,
+              originalRoutePath,
               _fsRouteType: 'static',
             }
           } else {
@@ -202,6 +216,7 @@ export async function getRouteNodesRecursive(
               fullPath: '',
               variableName: routePathToVariable(routePath),
               routePath,
+              originalRoutePath,
               isVirtual: true,
               _fsRouteType: 'static',
             }
@@ -235,13 +250,21 @@ export async function getRouteNodesRecursive(
             node.id = ensureLeadingUnderScore(fileNameWithoutExt)
           }
           const lastSegment = node.id
-          const routePath = `${parentRoutePath}/${removeLeadingSlash(lastSegment)}`
+          // Process the segment to handle escape sequences like [_]
+          const {
+            routePath: escapedSegment,
+            originalRoutePath: originalSegment,
+          } = determineInitialRoutePath(removeLeadingSlash(lastSegment))
+          const routePath = `${parentRoutePath}${escapedSegment}`
+          // Store the original path with brackets for escape detection
+          const originalRoutePath = `${parentRoutePath}${originalSegment}`
 
           const routeNode: RouteNode = {
             fullPath,
             filePath,
             variableName,
             routePath,
+            originalRoutePath,
             _fsRouteType: 'pathless_layout',
           }
 
diff --git a/packages/router-generator/tests/generator.test.ts b/packages/router-generator/tests/generator.test.ts
index 13aa39db3a..42594d7b0c 100644
--- a/packages/router-generator/tests/generator.test.ts
+++ b/packages/router-generator/tests/generator.test.ts
@@ -104,6 +104,17 @@ function rewriteConfigByFolderName(folderName: string, config: Config) {
     case 'virtual-config-file-default-export':
       config.virtualRouteConfig = './routes.ts'
       break
+    case 'virtual-with-escaped-underscore':
+      {
+        // Test case for escaped underscores in physical routes mounted via virtual config
+        // This ensures originalRoutePath is correctly prefixed when paths are updated
+        const virtualRouteConfig = rootRoute('__root.tsx', [
+          index('index.tsx'),
+          physical('/api', 'physical-routes'),
+        ])
+        config.virtualRouteConfig = virtualRouteConfig
+      }
+      break
     case 'types-disabled':
       config.disableTypes = true
       config.generatedRouteTree =
diff --git a/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routeTree.snapshot.ts b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routeTree.snapshot.ts
new file mode 100644
index 0000000000..53ba374b1a
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routeTree.snapshot.ts
@@ -0,0 +1,113 @@
+/* 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 { Route as rootRouteImport } from './routes/__root'
+import { Route as IndexRouteImport } from './routes/index'
+import { Route as nestedCallbackRouteImport } from './routes/nested/callback'
+import { Route as nestedAuthRouteImport } from './routes/nested/auth'
+import { Route as nestedHomeRouteImport } from './routes/nested/home'
+
+const IndexRoute = IndexRouteImport.update({
+  id: '/',
+  path: '/',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const nestedCallbackRoute = nestedCallbackRouteImport.update({
+  id: '/nested/_callback',
+  path: '/nested/_callback',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const nestedAuthRoute = nestedAuthRouteImport.update({
+  id: '/nested/_auth',
+  path: '/nested/_auth',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const nestedHomeRoute = nestedHomeRouteImport.update({
+  id: '/nested/',
+  path: '/nested/',
+  getParentRoute: () => rootRouteImport,
+} as any)
+
+export interface FileRoutesByFullPath {
+  '/': typeof IndexRoute
+  '/nested': typeof nestedHomeRoute
+  '/nested/_auth': typeof nestedAuthRoute
+  '/nested/_callback': typeof nestedCallbackRoute
+}
+export interface FileRoutesByTo {
+  '/': typeof IndexRoute
+  '/nested': typeof nestedHomeRoute
+  '/nested/_auth': typeof nestedAuthRoute
+  '/nested/_callback': typeof nestedCallbackRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/': typeof IndexRoute
+  '/nested/': typeof nestedHomeRoute
+  '/nested/_auth': typeof nestedAuthRoute
+  '/nested/_callback': typeof nestedCallbackRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/' | '/nested' | '/nested/_auth' | '/nested/_callback'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/' | '/nested' | '/nested/_auth' | '/nested/_callback'
+  id: '__root__' | '/' | '/nested/' | '/nested/_auth' | '/nested/_callback'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  IndexRoute: typeof IndexRoute
+  nestedHomeRoute: typeof nestedHomeRoute
+  nestedAuthRoute: typeof nestedAuthRoute
+  nestedCallbackRoute: typeof nestedCallbackRoute
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/': {
+      id: '/'
+      path: '/'
+      fullPath: '/'
+      preLoaderRoute: typeof IndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/nested/_callback': {
+      id: '/nested/_callback'
+      path: '/nested/_callback'
+      fullPath: '/nested/_callback'
+      preLoaderRoute: typeof nestedCallbackRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/nested/_auth': {
+      id: '/nested/_auth'
+      path: '/nested/_auth'
+      fullPath: '/nested/_auth'
+      preLoaderRoute: typeof nestedAuthRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/nested/': {
+      id: '/nested/'
+      path: '/nested'
+      fullPath: '/nested'
+      preLoaderRoute: typeof nestedHomeRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+  }
+}
+
+const rootRouteChildren: RootRouteChildren = {
+  IndexRoute: IndexRoute,
+  nestedHomeRoute: nestedHomeRoute,
+  nestedAuthRoute: nestedAuthRoute,
+  nestedCallbackRoute: nestedCallbackRoute,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
diff --git a/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/__root.tsx b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/__root.tsx
new file mode 100644
index 0000000000..87099187f8
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/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/virtual-inside-with-escaped-underscore/routes/index.tsx b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/index.tsx
new file mode 100644
index 0000000000..d1d6296bab
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/index.tsx
@@ -0,0 +1,2 @@
+import { createFileRoute } from '@tanstack/react-router'
+export const Route = createFileRoute('/')()
diff --git a/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/__virtual.ts b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/__virtual.ts
new file mode 100644
index 0000000000..391b0a3da0
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/__virtual.ts
@@ -0,0 +1,11 @@
+import {
+  defineVirtualSubtreeConfig,
+  index,
+  route,
+} from '@tanstack/virtual-file-routes'
+
+export default defineVirtualSubtreeConfig([
+  index('home.tsx'),
+  route('[_]auth', 'auth.tsx'),
+  route('[_]callback', 'callback.tsx'),
+])
diff --git a/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/auth.tsx b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/auth.tsx
new file mode 100644
index 0000000000..0da5aace4c
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/auth.tsx
@@ -0,0 +1,2 @@
+import { createFileRoute } from '@tanstack/react-router'
+export const Route = createFileRoute('/nested/_auth')()
diff --git a/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/callback.tsx b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/callback.tsx
new file mode 100644
index 0000000000..8885ecd48e
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/callback.tsx
@@ -0,0 +1,2 @@
+import { createFileRoute } from '@tanstack/react-router'
+export const Route = createFileRoute('/nested/_callback')()
diff --git a/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/home.tsx b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/home.tsx
new file mode 100644
index 0000000000..28c3b04574
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-inside-with-escaped-underscore/routes/nested/home.tsx
@@ -0,0 +1,2 @@
+import { createFileRoute } from '@tanstack/react-router'
+export const Route = createFileRoute('/nested/')()
diff --git a/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routeTree.snapshot.ts b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routeTree.snapshot.ts
new file mode 100644
index 0000000000..5726099cc7
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routeTree.snapshot.ts
@@ -0,0 +1,114 @@
+/* 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 { Route as rootRouteImport } from './routes/__root'
+import { Route as indexRouteImport } from './routes/index'
+import { Route as ApiIndexRouteImport } from './routes/physical-routes/index'
+import { Route as ApiChar91_Char93helloRouteImport } from './routes/physical-routes/[_]hello'
+import { Route as ApiChar91_Char93authDotrouteRouteImport } from './routes/physical-routes/[_]auth.route'
+
+const indexRoute = indexRouteImport.update({
+  id: '/',
+  path: '/',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const ApiIndexRoute = ApiIndexRouteImport.update({
+  id: '/api/',
+  path: '/api/',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const ApiChar91_Char93helloRoute = ApiChar91_Char93helloRouteImport.update({
+  id: '/api/_hello',
+  path: '/api/_hello',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const ApiChar91_Char93authDotrouteRoute =
+  ApiChar91_Char93authDotrouteRouteImport.update({
+    id: '/api/_auth',
+    path: '/api/_auth',
+    getParentRoute: () => rootRouteImport,
+  } as any)
+
+export interface FileRoutesByFullPath {
+  '/': typeof indexRoute
+  '/api/_auth': typeof ApiChar91_Char93authDotrouteRoute
+  '/api/_hello': typeof ApiChar91_Char93helloRoute
+  '/api': typeof ApiIndexRoute
+}
+export interface FileRoutesByTo {
+  '/': typeof indexRoute
+  '/api/_auth': typeof ApiChar91_Char93authDotrouteRoute
+  '/api/_hello': typeof ApiChar91_Char93helloRoute
+  '/api': typeof ApiIndexRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/': typeof indexRoute
+  '/api/_auth': typeof ApiChar91_Char93authDotrouteRoute
+  '/api/_hello': typeof ApiChar91_Char93helloRoute
+  '/api/': typeof ApiIndexRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/' | '/api/_auth' | '/api/_hello' | '/api'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/' | '/api/_auth' | '/api/_hello' | '/api'
+  id: '__root__' | '/' | '/api/_auth' | '/api/_hello' | '/api/'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  indexRoute: typeof indexRoute
+  ApiChar91_Char93authDotrouteRoute: typeof ApiChar91_Char93authDotrouteRoute
+  ApiChar91_Char93helloRoute: typeof ApiChar91_Char93helloRoute
+  ApiIndexRoute: typeof ApiIndexRoute
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/': {
+      id: '/'
+      path: '/'
+      fullPath: '/'
+      preLoaderRoute: typeof indexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/api/': {
+      id: '/api/'
+      path: '/api'
+      fullPath: '/api'
+      preLoaderRoute: typeof ApiIndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/api/_hello': {
+      id: '/api/_hello'
+      path: '/api/_hello'
+      fullPath: '/api/_hello'
+      preLoaderRoute: typeof ApiChar91_Char93helloRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/api/_auth': {
+      id: '/api/_auth'
+      path: '/api/_auth'
+      fullPath: '/api/_auth'
+      preLoaderRoute: typeof ApiChar91_Char93authDotrouteRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+  }
+}
+
+const rootRouteChildren: RootRouteChildren = {
+  indexRoute: indexRoute,
+  ApiChar91_Char93authDotrouteRoute: ApiChar91_Char93authDotrouteRoute,
+  ApiChar91_Char93helloRoute: ApiChar91_Char93helloRoute,
+  ApiIndexRoute: ApiIndexRoute,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
diff --git a/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/__root.tsx b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/__root.tsx
new file mode 100644
index 0000000000..9c657c7d5b
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/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/virtual-with-escaped-underscore/routes/index.tsx b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/index.tsx
new file mode 100644
index 0000000000..f077c2f494
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/')({
+  component: () => 'Hello',
+})
diff --git a/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/[_]auth.route.tsx b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/[_]auth.route.tsx
new file mode 100644
index 0000000000..9c3be05246
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/[_]auth.route.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/api/_auth')({
+  component: () => 'Auth Route',
+})
diff --git a/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/[_]hello.tsx b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/[_]hello.tsx
new file mode 100644
index 0000000000..a41e9110cf
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/[_]hello.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/api/_hello')({
+  component: () => 'Hello API',
+})
diff --git a/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/index.tsx b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/index.tsx
new file mode 100644
index 0000000000..b5e43f6788
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-with-escaped-underscore/routes/physical-routes/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/api/')({
+  component: () => 'API Index',
+})