diff --git a/packages/webview_flutter/webview_flutter_wkwebview/CHANGELOG.md b/packages/webview_flutter/webview_flutter_wkwebview/CHANGELOG.md
index 7b74c5e0f9e..11e10486544 100644
--- a/packages/webview_flutter/webview_flutter_wkwebview/CHANGELOG.md
+++ b/packages/webview_flutter/webview_flutter_wkwebview/CHANGELOG.md
@@ -1,3 +1,7 @@
+## 3.16.3
+
+* Fixes re-registering existing channels while removing Javascript channels.
+
 ## 3.16.2
 
 * Updates README to remove contributor-focused documentation.
diff --git a/packages/webview_flutter/webview_flutter_wkwebview/lib/src/webkit_webview_controller.dart b/packages/webview_flutter/webview_flutter_wkwebview/lib/src/webkit_webview_controller.dart
index a1f149ecdd1..ae254ef52fe 100644
--- a/packages/webview_flutter/webview_flutter_wkwebview/lib/src/webkit_webview_controller.dart
+++ b/packages/webview_flutter/webview_flutter_wkwebview/lib/src/webkit_webview_controller.dart
@@ -742,12 +742,16 @@ window.addEventListener("error", function(e) {
     _javaScriptChannelParams.keys.forEach(
       _webView.configuration.userContentController.removeScriptMessageHandler,
     );
-
-    _javaScriptChannelParams.remove(removedJavaScriptChannel);
+    final Map<String, WebKitJavaScriptChannelParams> remainingChannelParams =
+        Map<String, WebKitJavaScriptChannelParams>.from(
+      _javaScriptChannelParams,
+    );
+    remainingChannelParams.remove(removedJavaScriptChannel);
+    _javaScriptChannelParams.clear();
 
     await Future.wait(<Future<void>>[
       for (final JavaScriptChannelParams params
-          in _javaScriptChannelParams.values)
+          in remainingChannelParams.values)
         addJavaScriptChannel(params),
       // Zoom is disabled with a WKUserScript, so this adds it back if it was
       // removed above.
diff --git a/packages/webview_flutter/webview_flutter_wkwebview/pubspec.yaml b/packages/webview_flutter/webview_flutter_wkwebview/pubspec.yaml
index 658c46071e7..735efa3f86e 100644
--- a/packages/webview_flutter/webview_flutter_wkwebview/pubspec.yaml
+++ b/packages/webview_flutter/webview_flutter_wkwebview/pubspec.yaml
@@ -2,7 +2,7 @@ name: webview_flutter_wkwebview
 description: A Flutter plugin that provides a WebView widget based on Apple's WKWebView control.
 repository: https://github.com/flutter/packages/tree/main/packages/webview_flutter/webview_flutter_wkwebview
 issue_tracker: https://github.com/flutter/flutter/issues?q=is%3Aissue+is%3Aopen+label%3A%22p%3A+webview%22
-version: 3.16.2
+version: 3.16.3
 
 environment:
   sdk: ^3.5.0
diff --git a/packages/webview_flutter/webview_flutter_wkwebview/test/webkit_webview_controller_test.dart b/packages/webview_flutter/webview_flutter_wkwebview/test/webkit_webview_controller_test.dart
index d7aab4b5426..4e1208641e8 100644
--- a/packages/webview_flutter/webview_flutter_wkwebview/test/webkit_webview_controller_test.dart
+++ b/packages/webview_flutter/webview_flutter_wkwebview/test/webkit_webview_controller_test.dart
@@ -860,6 +860,72 @@ void main() {
       verifyNoMoreInteractions(mockUserContentController);
     });
 
+    test('removeJavaScriptChannel multiple times', () async {
+      final WebKitProxy webKitProxy = WebKitProxy(
+        createScriptMessageHandler: ({
+          required void Function(
+            WKUserContentController userContentController,
+            WKScriptMessage message,
+          ) didReceiveScriptMessage,
+        }) {
+          return WKScriptMessageHandler.detached(
+            didReceiveScriptMessage: didReceiveScriptMessage,
+          );
+        },
+      );
+
+      final WebKitJavaScriptChannelParams javaScriptChannelParams1 =
+          WebKitJavaScriptChannelParams(
+        name: 'name1',
+        onMessageReceived: (JavaScriptMessage message) {},
+        webKitProxy: webKitProxy,
+      );
+
+      final WebKitJavaScriptChannelParams javaScriptChannelParams2 =
+          WebKitJavaScriptChannelParams(
+        name: 'name2',
+        onMessageReceived: (JavaScriptMessage message) {},
+        webKitProxy: webKitProxy,
+      );
+
+      final MockWKUserContentController mockUserContentController =
+          MockWKUserContentController();
+
+      final WebKitWebViewController controller = createControllerWithMocks(
+        mockUserContentController: mockUserContentController,
+      );
+
+      await controller.addJavaScriptChannel(javaScriptChannelParams1);
+      await controller.addJavaScriptChannel(javaScriptChannelParams2);
+      reset(mockUserContentController);
+
+      await controller.removeJavaScriptChannel('name1');
+
+      verify(mockUserContentController.removeAllUserScripts());
+      verify(mockUserContentController.removeScriptMessageHandler('name1'));
+      verify(mockUserContentController.removeScriptMessageHandler('name2'));
+
+      verify(mockUserContentController.addScriptMessageHandler(
+        argThat(isA<WKScriptMessageHandler>()),
+        'name2',
+      ));
+
+      final WKUserScript userScript =
+          verify(mockUserContentController.addUserScript(captureAny))
+              .captured
+              .single as WKUserScript;
+      expect(userScript.source, 'window.name2 = webkit.messageHandlers.name2;');
+      expect(
+        userScript.injectionTime,
+        WKUserScriptInjectionTime.atDocumentStart,
+      );
+
+      await controller.removeJavaScriptChannel('name2');
+      verify(mockUserContentController.removeAllUserScripts());
+      verify(mockUserContentController.removeScriptMessageHandler('name2'));
+      verifyNoMoreInteractions(mockUserContentController);
+    });
+
     test('removeJavaScriptChannel with zoom disabled', () async {
       final WebKitProxy webKitProxy = WebKitProxy(
         createScriptMessageHandler: ({