diff --git a/packages/plugin-react/src/compilerRefresh.test.ts b/packages/plugin-react/src/compilerRefresh.test.ts
new file mode 100644
index 000000000..1de6f3030
--- /dev/null
+++ b/packages/plugin-react/src/compilerRefresh.test.ts
@@ -0,0 +1,83 @@
+import { mkdtemp, rm, writeFile } from 'node:fs/promises'
+import { tmpdir } from 'node:os'
+import { join } from 'node:path'
+import { createServer } from 'vite'
+import { expect, test } from 'vitest'
+import react from './index'
+
+const workerCode = `
+const Factory = { Values: <Value>(values: Value): Value => values }
+export enum MessageKind { Ready = 'ready', Complete = 'complete' }
+export const MessageKinds = Factory.Values(Object.values(MessageKind))
+`
+
+test('native compiler serves non-React TypeScript without refresh registrations', async () => {
+  const root = await mkdtemp(join(tmpdir(), 'react-compiler-refresh-'))
+  await writeFile(join(root, 'message.ts'), workerCode)
+  const server = await createServer({
+    root,
+    configFile: false,
+    logLevel: 'silent',
+    plugins: [react({ compiler: true })],
+  })
+  try {
+    const output = await server.transformRequest('/message.ts')
+    expect(output?.code).not.toContain('$RefreshReg$')
+    const module = await import(
+      `data:text/javascript,${encodeURIComponent(output!.code)}`
+    )
+    expect(module.MessageKinds).toEqual(['ready', 'complete'])
+  } finally {
+    await server.close()
+    await rm(root, { recursive: true, force: true })
+  }
+})
+
+test.each([
+  [
+    'component.tsx?query',
+    'export function App() { return <div /> }',
+    undefined,
+  ],
+  [
+    'component.ts',
+    'import { jsx } from "react/jsx-runtime"; export function App() { return jsx("div", {}) }',
+    undefined,
+  ],
+  [
+    'component.ts',
+    'import { jsxDEV } from "react/jsx-dev-runtime"; export function App() { return jsxDEV("div", {}) }',
+    undefined,
+  ],
+  [
+    'component.ts',
+    'import { jsx } from "@emotion/react/jsx-runtime"; export function App() { return jsx("div", {}) }',
+    '@emotion/react',
+  ],
+])(
+  'keeps refresh for %s with a JSX runtime',
+  async (id, code, jsxImportSource) => {
+    const server = await createServer({
+      configFile: false,
+      logLevel: 'silent',
+      plugins: [react({ compiler: true, jsxImportSource })],
+    })
+    try {
+      const plugin = server.config.plugins.find(
+        (p) => p.name === 'vite:react-compiler',
+      )!
+      const hook = plugin.transform!
+      const handler = typeof hook === 'function' ? hook : hook.handler
+      const output = await handler.call(
+        { environment: server.environments.client } as any,
+        code,
+        `/src/${id}`,
+      )
+      expect(
+        output && typeof output === 'object' ? output.code : output,
+      ).toContain('$RefreshReg$')
+    } finally {
+      await server.close()
+    }
+  },
+)
diff --git a/packages/plugin-react/src/index.ts b/packages/plugin-react/src/index.ts
index 778858962..fb413e26a 100644
--- a/packages/plugin-react/src/index.ts
+++ b/packages/plugin-react/src/index.ts
@@ -349,6 +349,14 @@ function createReactCompilerPlugin(
       },
       async handler(code, id) {
         const isClient = this.environment?.config.consumer !== 'server'
+        const filepath = id.split('?')[0]!
+        const jsxImportSource = reactOptions.jsxImportSource ?? 'react'
+        const useFastRefresh =
+          isClient &&
+          isFastRefreshEnabled() &&
+          (filepath.endsWith('x') ||
+            code.includes(`${jsxImportSource}/jsx-runtime`) ||
+            code.includes(`${jsxImportSource}/jsx-dev-runtime`))
         const shouldCompile =
           isClient &&
           (reactCompilerOptions.compilationMode === 'annotation'
@@ -358,12 +366,12 @@ function createReactCompilerPlugin(
         const { transform } =
           compiler ?? (await loadCompiler((message) => this.error(message)))
 
-        const result = await transform(id.split('?')[0]!, code, {
+        const result = await transform(filepath, code, {
           jsx: {
             runtime: reactOptions.jsxRuntime,
             development: jsxDevelopment,
             importSource: reactOptions.jsxImportSource,
-            refresh: isClient && isFastRefreshEnabled(),
+            refresh: useFastRefresh,
           },
           reactCompiler: shouldCompile ? reactCompilerOptions : false,
           sourcemap: this.environment