diff --git a/packages/vite/src/node/optimizer/optimizer.ts b/packages/vite/src/node/optimizer/optimizer.ts
index 5592c438ece552..9a331e9db90ab4 100644
--- a/packages/vite/src/node/optimizer/optimizer.ts
+++ b/packages/vite/src/node/optimizer/optimizer.ts
@@ -1,6 +1,8 @@
+import path from 'node:path'
 import colors from 'picocolors'
 import _debug from 'debug'
 import glob from 'fast-glob'
+import { FS_PREFIX } from '../constants'
 import { getHash } from '../utils'
 import { transformRequest } from '../server/transformRequest'
 import type { ResolvedConfig, ViteDevServer } from '..'
@@ -585,17 +587,21 @@ export async function preTransformOptimizeDepsEntries(
   server: ViteDevServer
 ): Promise<void> {
   const { config } = server
+  const { root } = config
   const { entries } = config.optimizeDeps
   if (entries) {
     const explicitEntries = await glob(entries, {
-      cwd: config.root,
+      cwd: root,
       ignore: ['**/node_modules/**', `**/${config.build.outDir}/**`],
       absolute: true
     })
     // TODO: should we restrict the entries to JS and HTML like the
     // scanner did? I think we can let the user chose any entry
     for (const entry of explicitEntries) {
-      transformRequest(entry, server, { ssr: false }).catch((e) => {
+      const url = entry.startsWith(root + '/')
+        ? entry.slice(root.length)
+        : path.posix.join(FS_PREFIX + entry)
+      transformRequest(url, server, { ssr: false }).catch((e) => {
         config.logger.error(e.message)
       })
     }