diff --git a/pkgs/jnigen/lib/src/bindings/renamer.dart b/pkgs/jnigen/lib/src/bindings/renamer.dart
index 2020a5cf9..572a2eb96 100644
--- a/pkgs/jnigen/lib/src/bindings/renamer.dart
+++ b/pkgs/jnigen/lib/src/bindings/renamer.dart
@@ -155,7 +155,7 @@ class Renamer implements Visitor<Classes, void> {
 class _ClassRenamer implements Visitor<ClassDecl, void> {
   final Config config;
   final Set<ClassDecl> renamed;
-  final Map<String, int> classNameCounts = {};
+  final Map<String, int> topLevelNameCounts = {};
   final Map<ClassDecl, Map<String, int>> nameCounts = {};
 
   _ClassRenamer(
@@ -192,7 +192,7 @@ class _ClassRenamer implements Visitor<ClassDecl, void> {
     final uniquifyName =
         config.outputConfig.dartConfig.structure == OutputStructure.singleFile;
     node.finalName = uniquifyName
-        ? _renameConflict(classNameCounts, className, _ElementKind.klass)
+        ? _renameConflict(topLevelNameCounts, className, _ElementKind.klass)
         : className;
     node.typeClassName = '\$${node.finalName}\$Type';
     node.nullableTypeClassName = '\$${node.finalName}\$NullableType';
@@ -201,14 +201,17 @@ class _ClassRenamer implements Visitor<ClassDecl, void> {
     // Rename fields before renaming methods. In case a method and a field have
     // identical names, the field will keep its original name and the
     // method will be renamed.
-    final fieldRenamer = _FieldRenamer(config, nameCounts[node]!);
+    final fieldRenamer = _FieldRenamer(
+      config,
+      uniquifyName && node.isTopLevel ? topLevelNameCounts : nameCounts[node]!,
+    );
     for (final field in node.fields) {
       field.accept(fieldRenamer);
     }
 
     final methodRenamer = _MethodRenamer(
       config,
-      nameCounts[node]!,
+      uniquifyName && node.isTopLevel ? topLevelNameCounts : nameCounts[node]!,
     );
     for (final method in node.methods) {
       method.accept(methodRenamer);
diff --git a/pkgs/jnigen/test/kotlin_test/bindings/kotlin.dart b/pkgs/jnigen/test/kotlin_test/bindings/kotlin.dart
index 2d8ea9bc6..6b1ab86c6 100644
--- a/pkgs/jnigen/test/kotlin_test/bindings/kotlin.dart
+++ b/pkgs/jnigen/test/kotlin_test/bindings/kotlin.dart
@@ -2396,3 +2396,77 @@ int topLevelSum(
           _id_topLevelSum as jni$_.JMethodIDPtr, i, i1)
       .integer;
 }
+
+final _TopLevelKt$1Class =
+    jni$_.JClass.forName(r'com/github/dart_lang/jnigen/subpackage/TopLevelKt');
+
+final _id_getTopLevelField$1 = _TopLevelKt$1Class.staticMethodId(
+  r'getTopLevelField',
+  r'()I',
+);
+
+final _getTopLevelField$1 = jni$_.ProtectedJniExtensions.lookup<
+        jni$_.NativeFunction<
+            jni$_.JniResult Function(
+              jni$_.Pointer<jni$_.Void>,
+              jni$_.JMethodIDPtr,
+            )>>('globalEnv_CallStaticIntMethod')
+    .asFunction<
+        jni$_.JniResult Function(
+          jni$_.Pointer<jni$_.Void>,
+          jni$_.JMethodIDPtr,
+        )>();
+
+/// from: `static public final int getTopLevelField()`
+int getTopLevelField$1() {
+  return _getTopLevelField$1(_TopLevelKt$1Class.reference.pointer,
+          _id_getTopLevelField$1 as jni$_.JMethodIDPtr)
+      .integer;
+}
+
+final _id_setTopLevelField$1 = _TopLevelKt$1Class.staticMethodId(
+  r'setTopLevelField',
+  r'(I)V',
+);
+
+final _setTopLevelField$1 = jni$_.ProtectedJniExtensions.lookup<
+            jni$_.NativeFunction<
+                jni$_.JThrowablePtr Function(jni$_.Pointer<jni$_.Void>,
+                    jni$_.JMethodIDPtr, jni$_.VarArgs<(jni$_.Int32,)>)>>(
+        'globalEnv_CallStaticVoidMethod')
+    .asFunction<
+        jni$_.JThrowablePtr Function(
+            jni$_.Pointer<jni$_.Void>, jni$_.JMethodIDPtr, int)>();
+
+/// from: `static public final void setTopLevelField(int i)`
+void setTopLevelField$1(
+  int i,
+) {
+  _setTopLevelField$1(_TopLevelKt$1Class.reference.pointer,
+          _id_setTopLevelField$1 as jni$_.JMethodIDPtr, i)
+      .check();
+}
+
+final _id_topLevel$1 = _TopLevelKt$1Class.staticMethodId(
+  r'topLevel',
+  r'()I',
+);
+
+final _topLevel$1 = jni$_.ProtectedJniExtensions.lookup<
+        jni$_.NativeFunction<
+            jni$_.JniResult Function(
+              jni$_.Pointer<jni$_.Void>,
+              jni$_.JMethodIDPtr,
+            )>>('globalEnv_CallStaticIntMethod')
+    .asFunction<
+        jni$_.JniResult Function(
+          jni$_.Pointer<jni$_.Void>,
+          jni$_.JMethodIDPtr,
+        )>();
+
+/// from: `static public final int topLevel()`
+int topLevel$1() {
+  return _topLevel$1(_TopLevelKt$1Class.reference.pointer,
+          _id_topLevel$1 as jni$_.JMethodIDPtr)
+      .integer;
+}
diff --git a/pkgs/jnigen/test/kotlin_test/kotlin/src/main/kotlin/com/github/dart_lang/jnigen/subpackage/TopLevel.kt b/pkgs/jnigen/test/kotlin_test/kotlin/src/main/kotlin/com/github/dart_lang/jnigen/subpackage/TopLevel.kt
new file mode 100644
index 000000000..6505f8715
--- /dev/null
+++ b/pkgs/jnigen/test/kotlin_test/kotlin/src/main/kotlin/com/github/dart_lang/jnigen/subpackage/TopLevel.kt
@@ -0,0 +1,14 @@
+/* Copyright (c) 2024, the Dart project authors. Please see the AUTHORS file
+ * for details. All rights reserved. Use of this source code is governed by a
+ * BSD-style license that can be found in the LICENSE file.
+ */
+
+package com.github.dart_lang.jnigen.subpackage
+
+// The same property and function defined in `../TopLevel.kt` to test renaming.
+
+var topLevelField: Int = 42
+
+fun topLevel(): Int {
+    return 42
+}
diff --git a/pkgs/jnigen/test/kotlin_test/runtime_test_registrant.dart b/pkgs/jnigen/test/kotlin_test/runtime_test_registrant.dart
index d946df915..827579ec5 100644
--- a/pkgs/jnigen/test/kotlin_test/runtime_test_registrant.dart
+++ b/pkgs/jnigen/test/kotlin_test/runtime_test_registrant.dart
@@ -24,10 +24,14 @@ void registerTests(String groupName, TestRunnerCallback test) {
 
     test('Top levels', () {
       expect(topLevel(), 42);
+      expect(topLevel$1(), 42);
       expect(topLevelSum(10, 20), 30);
       expect(getTopLevelField(), 42);
+      expect(getTopLevelField$1(), 42);
       setTopLevelField(30);
+      setTopLevelField$1(30);
       expect(getTopLevelField(), 30);
+      expect(getTopLevelField$1(), 30);
     });
 
     test('Generics', () {