diff --git a/packages/vite-node/src/utils.ts b/packages/vite-node/src/utils.ts
index b5c2d933d59e..d0b33edeb4cf 100644
--- a/packages/vite-node/src/utils.ts
+++ b/packages/vite-node/src/utils.ts
@@ -1,6 +1,7 @@
 import { fileURLToPath, pathToFileURL } from 'url'
-import { resolve } from 'pathe'
+import { relative, resolve } from 'pathe'
 import type { TransformResult } from 'vite'
+import { isNodeBuiltin } from 'mlly'
 import type { Arrayable, Nullable } from './types'
 
 export const isWindows = process.platform === 'win32'
@@ -45,6 +46,34 @@ export function isPrimitive(v: any) {
   return v !== Object(v)
 }
 
+export function pathFromRoot(root: string, filename: string) {
+  if (isNodeBuiltin(filename))
+    return filename
+
+  // don't replace with "/" on windows, "/C:/foo" is not a valid path
+  filename = filename.replace(/^\/@fs\//, isWindows ? '' : '/')
+
+  if (!filename.startsWith(root))
+    return filename
+
+  const relativePath = relative(root, filename)
+  // foo.js -> /foo.js
+  if (!relativePath.startsWith('/') && !relativePath.startsWith('.'))
+    return `/${relativePath}`
+
+  let index = 0
+  for (const char of relativePath) {
+    // ../../foo.js
+    //      ^ returns from here -> /foo.js
+    if (char !== '.' && char !== '/')
+      return relativePath.slice(index - 1)
+
+    index++
+  }
+
+  return relativePath
+}
+
 export function toFilePath(id: string, root: string): string {
   let absolute = id.startsWith('/@fs/')
     ? id.slice(4)
diff --git a/packages/vitest/src/runtime/mocker.ts b/packages/vitest/src/runtime/mocker.ts
index d14183ba119c..03981177547c 100644
--- a/packages/vitest/src/runtime/mocker.ts
+++ b/packages/vitest/src/runtime/mocker.ts
@@ -1,9 +1,9 @@
 import { existsSync, readdirSync } from 'fs'
 import { isNodeBuiltin } from 'mlly'
 import { basename, dirname, join, resolve } from 'pathe'
-import { normalizeRequestId, toFilePath } from 'vite-node/utils'
+import { normalizeRequestId, pathFromRoot, toFilePath } from 'vite-node/utils'
 import type { ModuleCacheMap } from 'vite-node/client'
-import { getAllMockableProperties, getType, getWorkerState, isWindows, mergeSlashes, slash } from '../utils'
+import { getAllMockableProperties, getType, getWorkerState, mergeSlashes, slash } from '../utils'
 import { distDir } from '../constants'
 import type { PendingSuiteMock } from '../types/mocker'
 import type { ExecuteOptions } from './execute'
@@ -142,14 +142,14 @@ export class VitestMocker {
   }
 
   public normalizePath(path: string) {
-    return normalizeRequestId(path.replace(this.root, ''), this.base).replace(/^\/@fs\//, isWindows ? '' : '/')
+    return pathFromRoot(this.root, normalizeRequestId(path, this.base))
   }
 
   public getFsPath(path: string, external: string | null) {
     if (external)
       return mergeSlashes(`/@fs/${path}`)
 
-    return normalizeRequestId(path.replace(this.root, ''))
+    return normalizeRequestId(path, this.base)
   }
 
   public resolveMockPath(mockPath: string, external: string | null) {
diff --git a/test/vite-config/src/src.ts b/test/vite-config/src/src.ts
new file mode 100644
index 000000000000..cb356468240d
--- /dev/null
+++ b/test/vite-config/src/src.ts
@@ -0,0 +1 @@
+export const foo = 'foo'
diff --git a/test/vite-config/src/test/root.test.ts b/test/vite-config/src/test/root.test.ts
index eabf33a1e79e..5f0edf39e390 100644
--- a/test/vite-config/src/test/root.test.ts
+++ b/test/vite-config/src/test/root.test.ts
@@ -1,5 +1,12 @@
-import { it } from 'vitest'
+import { expect, it, vi } from 'vitest'
+import { foo } from '../src'
+
+vi.mock('../src.ts', () => ({ foo: 'baz' }))
 
 it('should work', () => {
-  //
+  expect(1).toBe(1)
+})
+
+it('mocking with root works', () => {
+  expect(foo).toBe('baz')
 })