diff --git a/packages/start-plugin-core/src/rsbuild/planning.ts b/packages/start-plugin-core/src/rsbuild/planning.ts
index e6518ad2e6..2f79d4d0c5 100644
--- a/packages/start-plugin-core/src/rsbuild/planning.ts
+++ b/packages/start-plugin-core/src/rsbuild/planning.ts
@@ -73,6 +73,7 @@ export function createRsbuildEnvironmentPlan(opts: {
   clientOutputDirectory: string
   serverOutputDirectory: string
   publicBase: string
+  assetPrefix?: string | undefined
   serverFnProviderEnv: string
   environmentOverrides?: RsbuildEnvironmentOverrides
   scriptFormat?: ScriptFormat
@@ -106,6 +107,18 @@ export function createRsbuildEnvironmentPlan(opts: {
     )
   }
 
+  // When the user set output.assetPrefix, forward it. When they set
+  // server.base (and not assetPrefix), forward that via publicBase for
+  // backwards compatibility with the existing serverBase-precedence path.
+  // Otherwise leave assetPrefix unset so downstream plugins (e.g. Module
+  // Federation) and rsbuild's own default can take effect.
+  const clientAssetPrefix =
+    typeof opts.assetPrefix === 'string'
+      ? opts.assetPrefix
+      : opts.publicBase !== '/'
+        ? opts.publicBase
+        : undefined
+
   return {
     environments: {
       [RSBUILD_ENVIRONMENT_NAMES.client]: mergeRsbuildConfig(
@@ -134,7 +147,7 @@ export function createRsbuildEnvironmentPlan(opts: {
               media: `${RSBUILD_CLIENT_ASSETS_DIR}/media`,
               assets: `${RSBUILD_CLIENT_ASSETS_DIR}/assets`,
             },
-            assetPrefix: opts.publicBase,
+            assetPrefix: clientAssetPrefix,
           },
           resolve: {
             alias,
diff --git a/packages/start-plugin-core/src/rsbuild/plugin.ts b/packages/start-plugin-core/src/rsbuild/plugin.ts
index 3de4ed8c2f..b59e330c9a 100644
--- a/packages/start-plugin-core/src/rsbuild/plugin.ts
+++ b/packages/start-plugin-core/src/rsbuild/plugin.ts
@@ -118,6 +118,16 @@ export function tanStackStartRsbuild(
 
         const serverBase = rsbuildConfig.server?.base
         const assetPrefix = rsbuildConfig.output?.assetPrefix
+
+        // rsbuild normalizes output.assetPrefix to "/" when unset, same as
+        // server.base. Read the original config to tell "user set /" from
+        // "rsbuild filled in /" — when the user didn't set it, we forward
+        // undefined so rsbuild's own default and downstream plugins remain in
+        // control of the client environment's assetPrefix.
+        const originalConfig = api.getRsbuildConfig('original')
+        const userSetAssetPrefix =
+          originalConfig.output?.assetPrefix !== undefined
+
         const publicBase = normalizePublicBase(
           typeof serverBase === 'string'
             ? serverBase
@@ -171,6 +181,7 @@ export function tanStackStartRsbuild(
           clientOutputDirectory: resolvedStartConfig.outputDirectories.client,
           serverOutputDirectory: resolvedStartConfig.outputDirectories.server,
           publicBase: resolvedStartConfig.basePaths.publicBase,
+          assetPrefix: userSetAssetPrefix ? assetPrefix : undefined,
           serverFnProviderEnv,
           environmentOverrides: corePluginOpts.rsbuild?.environments,
           scriptFormat,
diff --git a/packages/start-plugin-core/tests/rsbuild/output-directory.test.ts b/packages/start-plugin-core/tests/rsbuild/output-directory.test.ts
index c0185a74eb..9a16ab00db 100644
--- a/packages/start-plugin-core/tests/rsbuild/output-directory.test.ts
+++ b/packages/start-plugin-core/tests/rsbuild/output-directory.test.ts
@@ -134,3 +134,74 @@ describe('createRsbuildEnvironmentPlan client output', () => {
     )
   })
 })
+
+describe('createRsbuildEnvironmentPlan assetPrefix', () => {
+  const baseOptions = {
+    root: '/app',
+    entryAliases: {
+      client: '/app/src/client.tsx',
+      server: '/app/src/server.ts',
+      start: '/app/src/start.ts',
+      router: '/app/src/router.tsx',
+      alias: {
+        'virtual:tanstack-start-client-entry': '/app/src/client.tsx',
+        'virtual:tanstack-start-server-entry': '/app/src/server.ts',
+        '#tanstack-start-entry': '/app/src/start.ts',
+        '#tanstack-router-entry': '/app/src/router.tsx',
+      },
+    },
+    clientOutputDirectory: 'dist/client',
+    serverOutputDirectory: 'dist/server',
+    publicBase: '/app/',
+    serverFnProviderEnv: 'ssr',
+  }
+
+  test('uses publicBase when assetPrefix is not provided and publicBase is not default', () => {
+    const plan = createRsbuildEnvironmentPlan(baseOptions)
+    expect(plan.environments.client!.output?.assetPrefix).toBe('/app/')
+  })
+
+  test('leaves assetPrefix undefined when neither configured and publicBase is default', () => {
+    const plan = createRsbuildEnvironmentPlan({
+      ...baseOptions,
+      publicBase: '/',
+    })
+    // Start forwards nothing so rsbuild's own default and downstream plugins
+    // (e.g. Module Federation gating on `=== undefined`) stay in control.
+    expect(plan.environments.client!.output?.assetPrefix).toBeUndefined()
+  })
+
+  test('forwards assetPrefix verbatim when explicitly set to "auto"', () => {
+    const plan = createRsbuildEnvironmentPlan({
+      ...baseOptions,
+      assetPrefix: 'auto',
+    })
+    expect(plan.environments.client!.output?.assetPrefix).toBe('auto')
+  })
+
+  test('uses assetPrefix when explicitly set to a path', () => {
+    const plan = createRsbuildEnvironmentPlan({
+      ...baseOptions,
+      assetPrefix: '/cdn/',
+    })
+    expect(plan.environments.client!.output?.assetPrefix).toBe('/cdn/')
+  })
+
+  test('uses assetPrefix when explicitly set to a full URL', () => {
+    const plan = createRsbuildEnvironmentPlan({
+      ...baseOptions,
+      assetPrefix: 'https://cdn.example.com/',
+    })
+    expect(plan.environments.client!.output?.assetPrefix).toBe(
+      'https://cdn.example.com/',
+    )
+  })
+
+  test('server environment never gets an assetPrefix', () => {
+    const plan = createRsbuildEnvironmentPlan({
+      ...baseOptions,
+      assetPrefix: 'https://cdn.example.com/',
+    })
+    expect(plan.environments.ssr!.output?.assetPrefix).toBeUndefined()
+  })
+})