diff --git a/packages/react-router/tests/router.test.tsx b/packages/react-router/tests/router.test.tsx
index d58dfe2126c..2214e9001eb 100644
--- a/packages/react-router/tests/router.test.tsx
+++ b/packages/react-router/tests/router.test.tsx
@@ -2670,6 +2670,144 @@ describe('rewriteBasepath utility', () => {
     expect(router.state.location.pathname).toBe('/users')
   })
 
+  it.each([
+    {
+      description: 'basepath with leading slash but without trailing slash',
+      basepath: '/api/v1',
+    },
+    {
+      description: 'basepath without leading slash but with trailing slash',
+      basepath: 'api/v1/',
+    },
+    {
+      description: 'basepath without leading and trailing slashes',
+      basepath: 'api/v1',
+    },
+  ])('should handle $description', async ({ basepath }) => {
+    const rootRoute = createRootRoute({
+      component: () => <Outlet />,
+    })
+
+    const usersRoute = createRoute({
+      getParentRoute: () => rootRoute,
+      path: '/users',
+      component: () => <div data-testid="users">Users</div>,
+    })
+
+    const routeTree = rootRoute.addChildren([usersRoute])
+
+    const router = createRouter({
+      routeTree,
+      history: createMemoryHistory({
+        initialEntries: ['/api/v1/users'],
+      }),
+      rewrite: rewriteBasepath({ basepath }),
+    })
+
+    render(<RouterProvider router={router} />)
+
+    await waitFor(() => {
+      expect(screen.getByTestId('users')).toBeInTheDocument()
+    })
+
+    expect(router.state.location.pathname).toBe('/users')
+  })
+
+  it.each([
+    { description: 'has trailing slash', basepath: '/my-app/' },
+    { description: 'has no trailing slash', basepath: '/my-app' },
+  ])(
+    'should not resolve to 404 when basepath $description and URL matches',
+    async ({ basepath }) => {
+      const rootRoute = createRootRoute({
+        component: () => <Outlet />,
+      })
+
+      const homeRoute = createRoute({
+        getParentRoute: () => rootRoute,
+        path: '/',
+        component: () => <div data-testid="home">Home</div>,
+      })
+
+      const usersRoute = createRoute({
+        getParentRoute: () => rootRoute,
+        path: '/users',
+        component: () => <div data-testid="users">Users</div>,
+      })
+
+      const routeTree = rootRoute.addChildren([homeRoute, usersRoute])
+
+      const router = createRouter({
+        routeTree,
+        history: createMemoryHistory({
+          initialEntries: ['/my-app/'],
+        }),
+        rewrite: rewriteBasepath({ basepath }),
+      })
+
+      render(<RouterProvider router={router} />)
+
+      await waitFor(() => {
+        expect(screen.getByTestId('home')).toBeInTheDocument()
+      })
+
+      expect(router.state.location.pathname).toBe('/')
+      expect(router.state.statusCode).toBe(200)
+    },
+  )
+
+  it.each([
+    { description: 'with trailing slash', basepath: '/my-app/' },
+    { description: 'without trailing slash', basepath: '/my-app' },
+  ])(
+    'should handle basepath $description when navigating to root path',
+    async ({ basepath }) => {
+      const rootRoute = createRootRoute({
+        component: () => <Outlet />,
+      })
+
+      const homeRoute = createRoute({
+        getParentRoute: () => rootRoute,
+        path: '/',
+        component: () => (
+          <div>
+            <Link to="/about" data-testid="about-link">
+              About
+            </Link>
+          </div>
+        ),
+      })
+
+      const aboutRoute = createRoute({
+        getParentRoute: () => rootRoute,
+        path: '/about',
+        component: () => <div data-testid="about">About</div>,
+      })
+
+      const routeTree = rootRoute.addChildren([homeRoute, aboutRoute])
+
+      const history = createMemoryHistory({ initialEntries: ['/my-app/'] })
+
+      const router = createRouter({
+        routeTree,
+        history,
+        rewrite: rewriteBasepath({ basepath }),
+      })
+
+      render(<RouterProvider router={router} />)
+
+      const aboutLink = await screen.findByTestId('about-link')
+      fireEvent.click(aboutLink)
+
+      await waitFor(() => {
+        expect(screen.getByTestId('about')).toBeInTheDocument()
+      })
+
+      expect(router.state.location.pathname).toBe('/about')
+      expect(history.location.pathname).toBe('/my-app/about')
+    },
+  )
+
   it('should handle empty basepath gracefully', async () => {
     const rootRoute = createRootRoute({
       component: () => <Outlet />,
diff --git a/packages/router-core/src/rewrite.ts b/packages/router-core/src/rewrite.ts
index c0cef0cc879..7ffb49b8e15 100644
--- a/packages/router-core/src/rewrite.ts
+++ b/packages/router-core/src/rewrite.ts
@@ -23,13 +23,28 @@ export function rewriteBasepath(opts: {
   caseSensitive?: boolean
 }) {
   const trimmedBasepath = trimPath(opts.basepath)
-  const regex = new RegExp(
-    `^/${trimmedBasepath}/`,
-    opts.caseSensitive ? '' : 'i',
-  )
+  const normalizedBasepath = `/${trimmedBasepath}`
+  const normalizedBasepathWithSlash = `${normalizedBasepath}/`
+  const checkBasepath = opts.caseSensitive
+    ? normalizedBasepath
+    : normalizedBasepath.toLowerCase()
+  const checkBasepathWithSlash = opts.caseSensitive
+    ? normalizedBasepathWithSlash
+    : normalizedBasepathWithSlash.toLowerCase()
+
   return {
     input: ({ url }) => {
-      url.pathname = url.pathname.replace(regex, '/')
+      const pathname = opts.caseSensitive
+        ? url.pathname
+        : url.pathname.toLowerCase()
+
+      // Handle exact basepath match (e.g., /my-app -> /)
+      if (pathname === checkBasepath) {
+        url.pathname = '/'
+      } else if (pathname.startsWith(checkBasepathWithSlash)) {
+        // Handle basepath with trailing content (e.g., /my-app/users -> /users)
+        url.pathname = url.pathname.slice(normalizedBasepath.length)
+      }
       return url
     },
     output: ({ url }) => {