diff --git a/docs/guide/api-environment-runtimes.md b/docs/guide/api-environment-runtimes.md
index 851175ce3bf6d5..e9b9a9a122fe4f 100644
--- a/docs/guide/api-environment-runtimes.md
+++ b/docs/guide/api-environment-runtimes.md
@@ -304,6 +304,8 @@ function createWorkerEnvironment(name, config, context) {
   const handlerToWorkerListener = new WeakMap()
 
   const workerHotChannel = {
+    // Worker threads post messages are not exposed over the network, skip server.fs checks
+    skipFsCheck: true,
     send: (data) => worker.postMessage(data),
     on: (event, handler) => {
       if (event === 'connection') return
diff --git a/packages/vite/src/node/config.ts b/packages/vite/src/node/config.ts
index a676474e667c92..0cba941e4e54d8 100644
--- a/packages/vite/src/node/config.ts
+++ b/packages/vite/src/node/config.ts
@@ -219,6 +219,7 @@ function defaultCreateClientDevEnvironment(
   return new DevEnvironment(name, config, {
     hot: true,
     transport: context.ws,
+    disableFetchModule: true,
   })
 }
 
diff --git a/packages/vite/src/node/server/environment.ts b/packages/vite/src/node/server/environment.ts
index 3ce3311e60a501..973e118daf9d38 100644
--- a/packages/vite/src/node/server/environment.ts
+++ b/packages/vite/src/node/server/environment.ts
@@ -1,6 +1,6 @@
-import type { FetchFunctionOptions, FetchResult } from 'vite/module-runner'
 import type { FSWatcher } from 'dep-types/chokidar'
 import colors from 'picocolors'
+import type { FetchFunctionOptions, FetchResult } from 'vite/module-runner'
 import {
   BaseEnvironment,
   getDefaultResolvedEnvironmentOptions,
@@ -45,6 +45,8 @@ export interface DevEnvironmentContext {
     inlineSourceMap?: boolean
   }
   depsOptimizer?: DepsOptimizer
+  /** @internal used for client environment */
+  disableFetchModule?: boolean
 }
 
 export class DevEnvironment extends BaseEnvironment {
@@ -56,6 +58,10 @@ export class DevEnvironment extends BaseEnvironment {
    * @internal
    */
   _remoteRunnerOptions: DevEnvironmentContext['remoteRunner']
+  /**
+   * @internal
+   */
+  _skipFsCheck: boolean
 
   get pluginContainer(): EnvironmentPluginContainer {
     if (!this._pluginContainer)
@@ -121,6 +127,11 @@ export class DevEnvironment extends BaseEnvironment {
     this._crawlEndFinder = setupOnCrawlEnd()
 
     this._remoteRunnerOptions = context.remoteRunner ?? {}
+    this._skipFsCheck = !!(
+      context.transport &&
+      !(isWebSocketServer in context.transport) &&
+      context.transport.skipFsCheck
+    )
 
     this.hot = context.transport
       ? isWebSocketServer in context.transport
@@ -130,6 +141,9 @@ export class DevEnvironment extends BaseEnvironment {
 
     this.hot.setInvokeHandler({
       fetchModule: (id, importer, options) => {
+        if (context.disableFetchModule) {
+          throw new Error('fetchModule is disabled in this environment')
+        }
         return this.fetchModule(id, importer, options)
       },
     })
@@ -210,12 +224,12 @@ export class DevEnvironment extends BaseEnvironment {
   }
 
   transformRequest(url: string): Promise<TransformResult | null> {
-    return transformRequest(this, url)
+    return transformRequest(this, url, { skipFsCheck: this._skipFsCheck })
   }
 
   async warmupRequest(url: string): Promise<void> {
     try {
-      await this.transformRequest(url)
+      await transformRequest(this, url, { skipFsCheck: true })
     } catch (e) {
       if (
         e?.code === ERR_OUTDATED_OPTIMIZED_DEP ||
diff --git a/packages/vite/src/node/server/hmr.ts b/packages/vite/src/node/server/hmr.ts
index 2c98a259f7bdde..d6ad9f4db8b383 100644
--- a/packages/vite/src/node/server/hmr.ts
+++ b/packages/vite/src/node/server/hmr.ts
@@ -87,6 +87,11 @@ export type HotChannelListener<T extends string = string> = (
 ) => void
 
 export interface HotChannel<Api = any> {
+  /**
+   * When true, the fs access check is skipped in fetchModule.
+   * Set this for transports that is not exposed over the network.
+   */
+  skipFsCheck?: boolean
   /**
    * Broadcast events to all clients
    */
@@ -1132,6 +1137,7 @@ export function createServerHotChannel(): ServerHotChannel {
   const outsideEmitter = new EventEmitter()
 
   return {
+    skipFsCheck: true,
     send(payload: HotPayload) {
       outsideEmitter.emit('send', payload)
     },
diff --git a/packages/vite/src/node/server/middlewares/transform.ts b/packages/vite/src/node/server/middlewares/transform.ts
index 8bdb124584d8e0..7f11f09fe7b49a 100644
--- a/packages/vite/src/node/server/middlewares/transform.ts
+++ b/packages/vite/src/node/server/middlewares/transform.ts
@@ -41,7 +41,12 @@ import {
   ERR_OUTDATED_OPTIMIZED_DEP,
   NULL_BYTE_PLACEHOLDER,
 } from '../../../shared/constants'
-import { checkServingAccess, respondWithAccessDenied } from './static'
+import type { ResolvedConfig } from '../../config'
+import {
+  checkLoadingAccess,
+  checkServingAccess,
+  respondWithAccessDenied,
+} from './static'
 
 const debugCache = createDebugger('vite:cache')
 
@@ -80,6 +85,16 @@ function deniedServingAccessForTransform(
   return false
 }
 
+export function isServerAccessDeniedForTransform(
+  config: ResolvedConfig,
+  id: string,
+): boolean {
+  if (rawRE.test(id) || urlRE.test(id) || inlineRE.test(id) || svgRE.test(id)) {
+    return checkLoadingAccess(config, id) !== 'allowed'
+  }
+  return false
+}
+
 /**
  * A middleware that short-circuits the middleware chain to serve cached transformed modules
  */
@@ -266,9 +281,7 @@ export function transformMiddleware(
         // resolve, load and transform using the plugin container
         const result = await transformRequest(environment, url, {
           html: req.headers.accept?.includes('text/html'),
-          allowId(id) {
-            return !deniedServingAccessForTransform(id, server, res, next)
-          },
+          skipFsCheck: environment._skipFsCheck,
         })
         if (result) {
           const depsOptimizer = environment.depsOptimizer
@@ -340,8 +353,24 @@ export function transformMiddleware(
         return next()
       }
       if (e?.code === ERR_DENIED_ID) {
-        // next() is called in ensureServingAccess
-        return
+        const id: string = e.id
+        let servingAccessResult = checkLoadingAccess(
+          server.config,
+          cleanUrl(id),
+        )
+        if (servingAccessResult === 'allowed') {
+          servingAccessResult = checkLoadingAccess(server.config, id)
+        }
+        if (servingAccessResult === 'denied') {
+          respondWithAccessDenied(id, server, res)
+          return true
+        }
+        if (servingAccessResult === 'fallback') {
+          next()
+          return true
+        }
+        servingAccessResult satisfies 'allowed'
+        throw new Error(`Unexpected access result for id ${id}`)
       }
       return next(e)
     }
diff --git a/packages/vite/src/node/server/transformRequest.ts b/packages/vite/src/node/server/transformRequest.ts
index 898d64146fc55c..ad9ed316a8467d 100644
--- a/packages/vite/src/node/server/transformRequest.ts
+++ b/packages/vite/src/node/server/transformRequest.ts
@@ -20,7 +20,7 @@ import {
 } from '../utils'
 import { ssrTransform } from '../ssr/ssrTransform'
 import { checkPublicFile } from '../publicDir'
-import { cleanUrl, unwrapId } from '../../shared/utils'
+import { cleanUrl, slash, unwrapId } from '../../shared/utils'
 import {
   applySourcemapIgnoreList,
   extractSourcemapFromFile,
@@ -29,6 +29,7 @@ import {
 import { isFileLoadingAllowed } from './middlewares/static'
 import { throwClosedServerError } from './pluginContainer'
 import type { DevEnvironment } from './environment'
+import { isServerAccessDeniedForTransform } from './middlewares/transform'
 
 export const ERR_LOAD_URL = 'ERR_LOAD_URL'
 export const ERR_LOAD_PUBLIC_URL = 'ERR_LOAD_PUBLIC_URL'
@@ -57,9 +58,10 @@ export interface TransformOptions {
    */
   html?: boolean
   /**
+   * Whether to skip the `server.fs` check.
    * @internal
    */
-  allowId?: (id: string) => boolean
+  skipFsCheck?: boolean
 }
 
 // TODO: This function could be moved to the DevEnvironment class.
@@ -253,8 +255,13 @@ async function loadAndTransform(
 
   const moduleGraph = environment.moduleGraph
 
-  if (options.allowId && !options.allowId(id)) {
+  if (
+    !options.skipFsCheck &&
+    id[0] !== '\0' &&
+    isServerAccessDeniedForTransform(config, id)
+  ) {
     const err: any = new Error(`Denied ID ${id}`)
+    err.id = id
     err.code = ERR_DENIED_ID
     throw err
   }
@@ -280,8 +287,8 @@ async function loadAndTransform(
     // only try the fallback if access is allowed, skip for out of root url
     // like /service-worker.js or /api/users
     if (
-      environment.config.consumer === 'server' ||
-      isFileLoadingAllowed(environment.getTopLevelConfig(), file)
+      options.skipFsCheck ||
+      isFileLoadingAllowed(environment.getTopLevelConfig(), slash(file))
     ) {
       try {
         code = await fsp.readFile(file, 'utf-8')
diff --git a/packages/vite/src/node/ssr/__tests__/fixtures/basic/file.js b/packages/vite/src/node/ssr/__tests__/fixtures/basic/file.js
new file mode 100644
index 00000000000000..60c71f346d9a3e
--- /dev/null
+++ b/packages/vite/src/node/ssr/__tests__/fixtures/basic/file.js
@@ -0,0 +1 @@
+export default 'ok'
diff --git a/packages/vite/src/node/ssr/__tests__/ssrLoadModule.spec.ts b/packages/vite/src/node/ssr/__tests__/ssrLoadModule.spec.ts
index d878ed09a7e6a6..0bbbba59cca772 100644
--- a/packages/vite/src/node/ssr/__tests__/ssrLoadModule.spec.ts
+++ b/packages/vite/src/node/ssr/__tests__/ssrLoadModule.spec.ts
@@ -376,3 +376,26 @@ test('buildStart before transform', async () => {
     ]
   `)
 })
+
+test('server.fs check is not applied to ssrLoadModule', async () => {
+  const server = await createServer({
+    configFile: false,
+    root,
+    logLevel: 'silent',
+    optimizeDeps: {
+      noDiscovery: true,
+    },
+    server: {
+      fs: {
+        allow: [
+          path.resolve(import.meta.dirname, './fixtures/named-overwrite-all'),
+        ],
+      },
+    },
+  })
+  onTestFinished(() => server.close())
+  await server.environments.ssr.pluginContainer.buildStart({})
+
+  const mod = await server.ssrLoadModule('/fixtures/basic/file.js')
+  expect(mod.default).toBe('ok')
+})
diff --git a/packages/vite/src/node/ssr/runtime/__tests__/fixture-outside.js b/packages/vite/src/node/ssr/runtime/__tests__/fixture-outside.js
new file mode 100644
index 00000000000000..b0c2b6333f05d9
--- /dev/null
+++ b/packages/vite/src/node/ssr/runtime/__tests__/fixture-outside.js
@@ -0,0 +1 @@
+export default 'error'
diff --git a/packages/vite/src/node/ssr/runtime/__tests__/server-runtime.spec.ts b/packages/vite/src/node/ssr/runtime/__tests__/server-runtime.spec.ts
index 2942856f780ea8..75e7c31af08ddb 100644
--- a/packages/vite/src/node/ssr/runtime/__tests__/server-runtime.spec.ts
+++ b/packages/vite/src/node/ssr/runtime/__tests__/server-runtime.spec.ts
@@ -1,5 +1,5 @@
 import { existsSync, readdirSync } from 'node:fs'
-import { posix, win32 } from 'node:path'
+import { posix, resolve, win32 } from 'node:path'
 import { fileURLToPath } from 'node:url'
 import { describe, expect, vi } from 'vitest'
 import { isWindows } from '../../../../shared/utils'
@@ -481,3 +481,18 @@ describe('virtual module hmr', async () => {
     })
   })
 })
+
+describe('server.fs check', async () => {
+  const it = await createModuleRunnerTester({
+    server: {
+      fs: {
+        allow: [resolve(import.meta.dirname, './fixtures/circular')],
+      },
+    },
+  })
+
+  it('it is not applied to the server module runner', async ({ runner }) => {
+    const mod = await runner.import('/fixtures/basic.js')
+    expect(mod.name).toBe('basic')
+  })
+})
diff --git a/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.invoke.spec.ts b/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.invoke.spec.ts
index cdca15c695afc6..6a649bbeb520d8 100644
--- a/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.invoke.spec.ts
+++ b/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.invoke.spec.ts
@@ -1,4 +1,5 @@
 import { BroadcastChannel, Worker } from 'node:worker_threads'
+import path from 'node:path'
 import { afterAll, beforeAll, describe, expect, it } from 'vitest'
 import type { BirpcReturn } from 'birpc'
 import { createBirpc } from 'birpc'
@@ -34,6 +35,9 @@ describe('running module runner inside a worker and using the ModuleRunnerTransp
         hmr: {
           port: 9610,
         },
+        fs: {
+          allow: [path.resolve(import.meta.dirname, './fixtures')],
+        },
       },
       environments: {
         worker: {
@@ -99,4 +103,13 @@ describe('running module runner inside a worker and using the ModuleRunnerTransp
     expect(output).not.toHaveProperty('result')
     expect(output.error).toContain('Error: Unknown invoke error')
   })
+
+  it('server.fs check is applied to the custom transport by default', async () => {
+    handleInvoke = (data: any) =>
+      server.environments.worker.hot.handleInvoke(data)
+
+    const output = await run('./fixture-outside.js')
+    expect(output).toHaveProperty('error')
+    expect(output.error).toContain('Failed to load url')
+  })
 })
diff --git a/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.spec.ts b/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.spec.ts
index 4af2fcb18b9c15..458e0718ff1757 100644
--- a/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.spec.ts
+++ b/packages/vite/src/node/ssr/runtime/__tests__/server-worker-runner.spec.ts
@@ -1,4 +1,5 @@
 import { BroadcastChannel, Worker } from 'node:worker_threads'
+import path from 'node:path'
 import { describe, expect, it, onTestFinished } from 'vitest'
 import type { HotChannel, HotChannelListener, HotPayload } from 'vite'
 import { DevEnvironment } from '../../..'
@@ -95,4 +96,48 @@ describe('running module runner inside a worker', () => {
       channel.postMessage({ id: './fixtures/default-string.ts' })
     })
   })
+
+  it('server.fs check is applied to the custom transport by default', async () => {
+    const worker = new Worker(
+      new URL('./fixtures/worker.mjs', import.meta.url),
+      { stdout: true },
+    )
+    await new Promise<void>((resolve, reject) => {
+      worker.on('message', () => resolve())
+      worker.on('error', reject)
+    })
+    const server = await createServer({
+      root: import.meta.dirname,
+      logLevel: 'error',
+      server: {
+        middlewareMode: true,
+        watch: null,
+        hmr: {
+          port: 9609,
+        },
+        fs: {
+          allow: [path.resolve(import.meta.dirname, './fixtures')],
+        },
+      },
+      environments: {
+        worker: {
+          dev: {
+            createEnvironment: (name, config) => {
+              return new DevEnvironment(name, config, {
+                hot: false,
+                transport: createWorkerTransport(worker),
+              })
+            },
+          },
+        },
+      },
+    })
+    onTestFinished(async () => {
+      await Promise.allSettled([server.close(), worker.terminate()])
+    })
+
+    await expect(
+      server.environments.worker.transformRequest('./fixture-outside.js'),
+    ).rejects.toThrow('Failed to load url')
+  })
 })
diff --git a/packages/vite/src/node/ssr/runtime/serverModuleRunner.ts b/packages/vite/src/node/ssr/runtime/serverModuleRunner.ts
index 59d7bc2050521f..a2b16fbdf7b4d7 100644
--- a/packages/vite/src/node/ssr/runtime/serverModuleRunner.ts
+++ b/packages/vite/src/node/ssr/runtime/serverModuleRunner.ts
@@ -1,11 +1,11 @@
 import { existsSync, readFileSync } from 'node:fs'
-import { ModuleRunner } from 'vite/module-runner'
+import type { HotPayload } from 'types/hmrPayload'
 import type {
   ModuleEvaluator,
   ModuleRunnerHmr,
   ModuleRunnerOptions,
 } from 'vite/module-runner'
-import type { HotPayload } from 'types/hmrPayload'
+import { ModuleRunner } from 'vite/module-runner'
 import type { DevEnvironment } from '../../server/environment'
 import type {
   HotChannelClient,
diff --git a/packages/vite/src/node/ssr/ssrModuleLoader.ts b/packages/vite/src/node/ssr/ssrModuleLoader.ts
index 6d431704446053..8153944f904a03 100644
--- a/packages/vite/src/node/ssr/ssrModuleLoader.ts
+++ b/packages/vite/src/node/ssr/ssrModuleLoader.ts
@@ -1,6 +1,6 @@
 import colors from 'picocolors'
-import type { EvaluatedModuleNode } from 'vite/module-runner'
 import { ESModulesEvaluator, ModuleRunner } from 'vite/module-runner'
+import type { EvaluatedModuleNode } from 'vite/module-runner'
 import type { ViteDevServer } from '../server'
 import { unwrapId } from '../../shared/utils'
 import type { DevEnvironment } from '../server/environment'
diff --git a/playground/fs-serve/__tests__/commonTests.ts b/playground/fs-serve/__tests__/commonTests.ts
index 5e401401a3060e..1493aac0271b15 100644
--- a/playground/fs-serve/__tests__/commonTests.ts
+++ b/playground/fs-serve/__tests__/commonTests.ts
@@ -1,4 +1,7 @@
 import http from 'node:http'
+import path from 'node:path'
+import { pathToFileURL } from 'node:url'
+import { setTimeout } from 'node:timers/promises'
 import {
   afterEach,
   beforeAll,
@@ -462,6 +465,72 @@ describe('cross origin', () => {
   })
 })
 
+describe.runIf(isServe)('fetchModule via WebSocket', () => {
+  const root = path.resolve(
+    import.meta.dirname.replace('playground', 'playground-temp'),
+    '..',
+  )
+
+  const fetchModuleViaWebSocket = async (filePath: string) => {
+    const resolvedPath = path.resolve(root, filePath)
+    const token = viteServer.config.webSocketToken
+    const wsUrl = viteTestUrl.replace('http', 'ws')
+    const ws = new WebSocket(`${wsUrl}?token=${token}`, ['vite-hmr'])
+
+    try {
+      return await Promise.race([
+        new Promise<any>((resolve, reject) => {
+          ws.on('open', () => {
+            ws.send(
+              JSON.stringify({
+                type: 'custom',
+                event: 'vite:invoke',
+                data: {
+                  name: 'fetchModule',
+                  id: 'send:1',
+                  data: [pathToFileURL(resolvedPath).href],
+                },
+              }),
+            )
+          })
+
+          ws.on('message', (raw: Buffer) => {
+            const parsed = JSON.parse(raw.toString())
+            if (
+              parsed.type === 'custom' &&
+              parsed.event === 'vite:invoke' &&
+              parsed.data?.id === 'response:1'
+            ) {
+              resolve(parsed.data.data)
+            }
+          })
+
+          ws.on('error', (err) => {
+            reject(err)
+          })
+        }),
+        setTimeout(10_000).then(() =>
+          Promise.reject(new Error('WebSocket response timed out')),
+        ),
+      ])
+    } finally {
+      ws.close()
+    }
+  }
+
+  test('should not read files inside allowed directories as fetchModule is disabled', async () => {
+    const result = await fetchModuleViaWebSocket('root/src/safe.txt?raw')
+    expect(result.result).toBeUndefined()
+    expect(result.error).toBeTruthy()
+  })
+
+  test('should not read files outside allowed directories', async () => {
+    const result = await fetchModuleViaWebSocket('root/unsafe.txt?raw')
+    expect(result.result).toBeUndefined()
+    expect(result.error).toBeTruthy()
+  })
+})
+
 describe.runIf(!isServe)('preview HTML', () => {
   test('unsafe HTML fetch', async () => {
     await expect.poll(() => page.textContent('.unsafe-fetch-html')).toBe('')