diff --git a/cmd/internal/migrations/v3/filesystem_middleware.go b/cmd/internal/migrations/v3/filesystem_middleware.go
index a8c502f..79e7373 100644
--- a/cmd/internal/migrations/v3/filesystem_middleware.go
+++ b/cmd/internal/migrations/v3/filesystem_middleware.go
@@ -11,6 +11,14 @@ import (
 	"github.com/gofiber/cli/cmd/internal"
 )
 
+var (
+	reFilesystemNew          = regexp.MustCompile(`filesystem\.New\s*\(`)
+	reFilesystemRootHTTP     = regexp.MustCompile(`Root:\s*http.Dir\(([^)]+)\)`)
+	reFilesystemRoot         = regexp.MustCompile(`Root:\s*([^,\n]+)`)
+	reFilesystemIndex        = regexp.MustCompile(`Index:\s*([^,\n]+)`)
+	reFilesystemNotFoundFile = regexp.MustCompile(`(?m)^(\s*)(NotFoundFile:\s*[^,\n]+)(,?)`)
+)
+
 func MigrateFilesystemMiddleware(cmd *cobra.Command, cwd string, _, _ *semver.Version) error {
 	changed, err := internal.ChangeFileContent(cwd, func(content string) string {
 		content = strings.ReplaceAll(content,
@@ -20,19 +28,23 @@ func MigrateFilesystemMiddleware(cmd *cobra.Command, cwd string, _, _ *semver.Ve
 			"github.com/gofiber/fiber/v3/middleware/filesystem",
 			"github.com/gofiber/fiber/v3/middleware/static")
 
-		reNew := regexp.MustCompile(`filesystem\.New\s*\(`)
-		content = reNew.ReplaceAllString(content, `static.New("", `)
+		content = reFilesystemNew.ReplaceAllString(content, `static.New("", `)
 
 		content = strings.ReplaceAll(content, "filesystem.Config{", "static.Config{")
 
-		reRootHTTP := regexp.MustCompile(`Root:\s*http.Dir\(([^)]+)\)`)
-		content = reRootHTTP.ReplaceAllString(content, `FS: os.DirFS($1)`)
+		content = reFilesystemRootHTTP.ReplaceAllString(content, `FS: os.DirFS($1)`)
+
+		content = reFilesystemRoot.ReplaceAllString(content, `FS: os.DirFS($1)`)
 
-		reRoot := regexp.MustCompile(`Root:\s*([^,\n]+)`)
-		content = reRoot.ReplaceAllString(content, `FS: os.DirFS($1)`)
+		content = reFilesystemIndex.ReplaceAllString(content, `IndexNames: []string{$1}`)
 
-		reIndex := regexp.MustCompile(`Index:\s*([^,\n]+)`)
-		content = reIndex.ReplaceAllString(content, `IndexNames: []string{$1}`)
+		// Handle NotFoundFile migration - comment it out and add TODO for NotFoundHandler
+		// Only migrate if not already migrated (check for TODO comment)
+		if !strings.Contains(content, "TODO: Migrate to NotFoundHandler") {
+			content = reFilesystemNotFoundFile.ReplaceAllString(content,
+				`$1// TODO: Migrate to NotFoundHandler (fiber.Handler) - NotFoundFile is deprecated
+$1// $2$3`)
+		}
 
 		return content
 	})
diff --git a/cmd/internal/migrations/v3/filesystem_middleware_test.go b/cmd/internal/migrations/v3/filesystem_middleware_test.go
index 9a47c38..6b649db 100644
--- a/cmd/internal/migrations/v3/filesystem_middleware_test.go
+++ b/cmd/internal/migrations/v3/filesystem_middleware_test.go
@@ -3,6 +3,7 @@ package v3_test
 import (
 	"bytes"
 	"os"
+	"strings"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
@@ -40,3 +41,79 @@ func main() {
 	assert.Contains(t, content, `IndexNames: []string{"index.html"}`)
 	assert.Contains(t, buf.String(), "Migrating filesystem middleware")
 }
+
+func Test_MigrateFilesystemMiddleware_WithNotFoundFile(t *testing.T) {
+	t.Parallel()
+
+	dir, err := os.MkdirTemp("", "mfs-notfound")
+	require.NoError(t, err)
+	defer func() { require.NoError(t, os.RemoveAll(dir)) }()
+
+	file := writeTempFile(t, dir, `package main
+import (
+    "github.com/gofiber/fiber/v2/middleware/filesystem"
+    "net/http"
+)
+func main() {
+    app.All("/*", filesystem.New(filesystem.Config{
+        Root:         http.Dir("./dist"),
+        NotFoundFile: "index.html",
+        Index:        "index.html",
+    }))
+}`)
+
+	var buf bytes.Buffer
+	cmd := newCmd(&buf)
+	require.NoError(t, v3.MigrateFilesystemMiddleware(cmd, dir, nil, nil))
+
+	content := readFile(t, file)
+	// Check that NotFoundFile is commented out
+	assert.Contains(t, content, "// NotFoundFile: \"index.html\"")
+	// Check that TODO comment is added
+	assert.Contains(t, content, "// TODO: Migrate to NotFoundHandler (fiber.Handler) - NotFoundFile is deprecated")
+	// Check that static migration happened
+	assert.Contains(t, content, `static.New("", static.Config{`)
+	assert.Contains(t, content, `FS: os.DirFS("./dist")`)
+	assert.Contains(t, content, `IndexNames: []string{"index.html"}`)
+}
+
+func Test_MigrateFilesystemMiddleware_NotFoundFileIdempotent(t *testing.T) {
+	t.Parallel()
+
+	dir, err := os.MkdirTemp("", "mfs-idempotent")
+	require.NoError(t, err)
+	defer func() { require.NoError(t, os.RemoveAll(dir)) }()
+
+	file := writeTempFile(t, dir, `package main
+import (
+    "github.com/gofiber/fiber/v2/middleware/filesystem"
+    "net/http"
+)
+func main() {
+    app.All("/*", filesystem.New(filesystem.Config{
+        Root:         http.Dir("./dist"),
+        NotFoundFile: "index.html",
+        Index:        "index.html",
+    }))
+}`)
+
+	var buf bytes.Buffer
+	cmd := newCmd(&buf)
+
+	// First migration
+	require.NoError(t, v3.MigrateFilesystemMiddleware(cmd, dir, nil, nil))
+	firstContent := readFile(t, file)
+
+	// Second migration - should be idempotent
+	buf.Reset()
+	require.NoError(t, v3.MigrateFilesystemMiddleware(cmd, dir, nil, nil))
+	secondContent := readFile(t, file)
+
+	// Content should be exactly the same after second migration
+	assert.Equal(t, firstContent, secondContent, "Migration should be idempotent")
+
+	// Verify the TODO comment is only present once
+	assert.Equal(t, 1, strings.Count(secondContent, "TODO: Migrate to NotFoundHandler"))
+	// Verify the NotFoundFile comment is only present once
+	assert.Equal(t, 1, strings.Count(secondContent, "// NotFoundFile:"))
+}