diff --git a/integration/vite-presets-test.ts b/integration/vite-presets-test.ts
index 34a2c3933f..3c88154853 100644
--- a/integration/vite-presets-test.ts
+++ b/integration/vite-presets-test.ts
@@ -226,6 +226,7 @@ test.describe("Vite / presets", async () => {
         "serverBundles",
         "serverModuleFormat",
         "ssr",
+        "unstable_rootRouteFile",
         "unstable_routeConfig",
       ]);
 
diff --git a/packages/react-router-dev/config/config.ts b/packages/react-router-dev/config/config.ts
index 68ef25cb12..98353026b8 100644
--- a/packages/react-router-dev/config/config.ts
+++ b/packages/react-router-dev/config/config.ts
@@ -264,6 +264,10 @@ export type ResolvedReactRouterConfig = Readonly<{
    * SPA without server-rendering. Default's to `true`.
    */
   ssr: boolean;
+  /**
+   * The absolute path to the root route file.
+   */
+  unstable_rootRouteFile: string;
   /**
    * The resolved array of route config entries exported from `routes.ts`
    */
@@ -345,6 +349,8 @@ type Result<T> =
       error: string;
     };
 
+type ConfigResult = Result<ResolvedReactRouterConfig>;
+
 function ok<T>(value: T): Result<T> {
   return { ok: true, value };
 }
@@ -365,7 +371,7 @@ async function resolveConfig({
   reactRouterConfigFile?: string;
   skipRoutes?: boolean;
   validateConfig?: ValidateConfigFunction;
-}): Promise<Result<ResolvedReactRouterConfig>> {
+}): Promise<ConfigResult> {
   let reactRouterUserConfig: ReactRouterConfig = {};
 
   if (reactRouterConfigFile) {
@@ -506,7 +512,7 @@ async function resolveConfig({
   let appDirectory = Path.resolve(root, userAppDirectory || "app");
   let buildDirectory = Path.resolve(root, userBuildDirectory);
 
-  let rootRouteFile = findEntry(appDirectory, "root");
+  let rootRouteFile = findEntry(appDirectory, "root", { absolute: true });
   if (!rootRouteFile) {
     let rootRouteDisplayPath = Path.relative(
       root,
@@ -556,7 +562,7 @@ async function resolveConfig({
         {
           id: "root",
           path: "",
-          file: rootRouteFile,
+          file: Path.relative(appDirectory, rootRouteFile),
           children: result.routeConfig,
         },
       ];
@@ -609,6 +615,7 @@ async function resolveConfig({
     serverBundles,
     serverModuleFormat,
     ssr,
+    unstable_rootRouteFile: rootRouteFile,
     unstable_routeConfig: routeConfig,
   } satisfies ResolvedReactRouterConfig);
 
@@ -622,7 +629,7 @@ async function resolveConfig({
 type ChokidarEventName = ChokidarEmitArgs[0];
 
 type ChangeHandler = (args: {
-  result: Result<ResolvedReactRouterConfig>;
+  result: ConfigResult;
   configCodeChanged: boolean;
   routeConfigCodeChanged: boolean;
   configChanged: boolean;
@@ -632,7 +639,7 @@ type ChangeHandler = (args: {
 }) => void;
 
 export type ConfigLoader = {
-  getConfig: () => Promise<Result<ResolvedReactRouterConfig>>;
+  getConfig: () => Promise<ConfigResult>;
   onChange: (handler: ChangeHandler) => () => void;
   close: () => Promise<void>;
 };
diff --git a/packages/react-router-dev/vite/rsc/plugin.ts b/packages/react-router-dev/vite/rsc/plugin.ts
index 3c2b15efa4..202cfe4984 100644
--- a/packages/react-router-dev/vite/rsc/plugin.ts
+++ b/packages/react-router-dev/vite/rsc/plugin.ts
@@ -315,6 +315,7 @@ export function reactRouterRSCVitePlugin(): Vite.PluginOption[] {
           id,
           viteCommand,
           routeIdByFile,
+          rootRouteFile: config.unstable_rootRouteFile,
           viteEnvironment: this.environment,
         });
       },
diff --git a/packages/react-router-dev/vite/rsc/virtual-route-config.ts b/packages/react-router-dev/vite/rsc/virtual-route-config.ts
index a9a4352b4a..1edddcb042 100644
--- a/packages/react-router-dev/vite/rsc/virtual-route-config.ts
+++ b/packages/react-router-dev/vite/rsc/virtual-route-config.ts
@@ -28,7 +28,7 @@ export function createVirtualRouteConfig({
     const routeId = route.id || createRouteId(route.file, appDirectory);
     routeIdByFile.set(routeFile, routeId);
     code += `lazy: () => import(${JSON.stringify(
-      `${routeFile}?route-module${routeId === "root" ? "&root-route=true" : ""}`,
+      `${routeFile}?route-module`,
     )}),`;
 
     code += `id: ${JSON.stringify(routeId)},`;
diff --git a/packages/react-router-dev/vite/rsc/virtual-route-modules.ts b/packages/react-router-dev/vite/rsc/virtual-route-modules.ts
index 0dc93141ff..5c5cdea04e 100644
--- a/packages/react-router-dev/vite/rsc/virtual-route-modules.ts
+++ b/packages/react-router-dev/vite/rsc/virtual-route-modules.ts
@@ -97,40 +97,54 @@ export function transformVirtualRouteModules({
   code,
   viteCommand,
   routeIdByFile,
+  rootRouteFile,
   viteEnvironment,
 }: {
   id: string;
   code: string;
   viteCommand: ViteCommand;
   routeIdByFile: Map<string, string>;
+  rootRouteFile: string;
   viteEnvironment: Vite.Environment;
 }) {
   if (isVirtualRouteModuleId(id) || routeIdByFile.has(id)) {
     return createVirtualRouteModuleCode({
       id,
       code,
+      rootRouteFile,
       viteCommand,
       viteEnvironment,
     });
   }
 
   if (isVirtualServerRouteModuleId(id)) {
-    return createVirtualServerRouteModuleCode({ id, code, viteEnvironment });
+    return createVirtualServerRouteModuleCode({
+      id,
+      code,
+      viteEnvironment,
+    });
   }
 
   if (isVirtualClientRouteModuleId(id)) {
-    return createVirtualClientRouteModuleCode({ id, code, viteCommand });
+    return createVirtualClientRouteModuleCode({
+      id,
+      code,
+      rootRouteFile,
+      viteCommand,
+    });
   }
 }
 
 async function createVirtualRouteModuleCode({
   id,
   code: routeSource,
+  rootRouteFile,
   viteCommand,
   viteEnvironment,
 }: {
   id: string;
   code: string;
+  rootRouteFile: string;
   viteCommand: ViteCommand;
   viteEnvironment: Vite.Environment;
 }) {
@@ -183,7 +197,10 @@ async function createVirtualRouteModuleCode({
     }
   }
 
-  if (isRootRouteId(id) && !staticExports.includes("ErrorBoundary")) {
+  if (
+    isRootRouteFile({ id, rootRouteFile }) &&
+    !staticExports.includes("ErrorBoundary")
+  ) {
     code += `export { ErrorBoundary } from "${clientModuleId}";\n`;
   }
 
@@ -236,10 +253,12 @@ function createVirtualServerRouteModuleCode({
 function createVirtualClientRouteModuleCode({
   id,
   code: routeSource,
+  rootRouteFile,
   viteCommand,
 }: {
   id: string;
   code: string;
+  rootRouteFile: string;
   viteCommand: ViteCommand;
 }) {
   const { staticExports, isServerFirstRoute, hasClientExports } =
@@ -256,7 +275,10 @@ function createVirtualClientRouteModuleCode({
   const generatorResult = babel.generate(clientRouteModuleAst);
   generatorResult.code = '"use client";' + generatorResult.code;
 
-  if (isRootRouteId(id) && !staticExports.includes("ErrorBoundary")) {
+  if (
+    isRootRouteFile({ id, rootRouteFile }) &&
+    !staticExports.includes("ErrorBoundary")
+  ) {
     const hasRootLayout = staticExports.includes("Layout");
     generatorResult.code += `\nimport { createElement as __rr_createElement } from "react";\n`;
     generatorResult.code += `import { UNSAFE_RSCDefaultRootErrorBoundary } from "react-router";\n`;
@@ -288,15 +310,11 @@ export function parseRouteExports(code: string) {
 }
 
 function getVirtualClientModuleId(id: string): string {
-  return `${id.split("?")[0]}?client-route-module${isRootRouteId(id) ? "&root-route=true" : ""}`;
+  return `${id.split("?")[0]}?client-route-module`;
 }
 
 function getVirtualServerModuleId(id: string): string {
-  return `${id.split("?")[0]}?server-route-module${isRootRouteId(id) ? "&root-route=true" : ""}`;
-}
-
-function isRootRouteId(id: string): boolean {
-  return /(\?|&)root-route=true(&|$)/.test(id);
+  return `${id.split("?")[0]}?server-route-module`;
 }
 
 function isVirtualRouteModuleId(id: string): boolean {
@@ -310,3 +328,14 @@ export function isVirtualClientRouteModuleId(id: string): boolean {
 function isVirtualServerRouteModuleId(id: string): boolean {
   return /(\?|&)server-route-module(&|$)/.test(id);
 }
+
+function isRootRouteFile({
+  id,
+  rootRouteFile,
+}: {
+  id: string;
+  rootRouteFile: string;
+}): boolean {
+  const filePath = id.split("?")[0];
+  return filePath === rootRouteFile;
+}