diff --git a/packages/go_router/lib/src/builder.dart b/packages/go_router/lib/src/builder.dart
index 7594513e8264..13a4f06ba6c6 100644
--- a/packages/go_router/lib/src/builder.dart
+++ b/packages/go_router/lib/src/builder.dart
@@ -2,6 +2,7 @@
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
+import 'package:flutter/foundation.dart';
 import 'package:flutter/widgets.dart';
 
 import 'configuration.dart';
@@ -135,6 +136,7 @@ class _CustomNavigator extends StatefulWidget {
     required this.errorBuilder,
     required this.errorPageBuilder,
     required this.requestFocus,
+    this.navigatorActive,
   });
 
   final GlobalKey<NavigatorState> navigatorKey;
@@ -153,6 +155,7 @@ class _CustomNavigator extends StatefulWidget {
   final GoRouterWidgetBuilder? errorBuilder;
   final GoRouterPageBuilder? errorPageBuilder;
   final bool requestFocus;
+  final ValueListenable<bool>? navigatorActive;
 
   @override
   State<StatefulWidget> createState() => _CustomNavigatorState();
@@ -276,8 +279,9 @@ class _CustomNavigatorState extends State<_CustomNavigator> {
             ShellRouteMatch match,
             RouteMatchList matchList,
             List<NavigatorObserver>? observers,
-            String? restorationScopeId,
-          ) {
+            String? restorationScopeId, {
+            ValueListenable<bool>? navigatorActive,
+          }) {
             return PopScope(
               // Prevent ShellRoute from being popped, for example
               // by an iOS back gesture, when the route has active sub-routes.
@@ -294,6 +298,7 @@ class _CustomNavigatorState extends State<_CustomNavigator> {
                 configuration: widget.configuration,
                 observers: observers ?? const <NavigatorObserver>[],
                 onPopPageWithRouteMatch: widget.onPopPageWithRouteMatch,
+                navigatorActive: navigatorActive,
                 // This is used to recursively build pages under this shell route.
                 errorBuilder: widget.errorBuilder,
                 errorPageBuilder: widget.errorPageBuilder,
@@ -368,12 +373,15 @@ class _CustomNavigatorState extends State<_CustomNavigator> {
   Page<Object?> _buildPlatformAdapterPage(BuildContext context, GoRouterState state, Widget child) {
     // build the page based on app type
     _cacheAppType(context);
+    final Widget pageChild = widget.navigatorActive == null
+        ? child
+        : _BranchNavigatorPopScope(navigatorActive: widget.navigatorActive!, child: child);
     return _pageBuilderForAppType!(
       key: state.pageKey,
       name: state.name ?? state.path,
       arguments: <String, String>{...state.pathParameters, ...state.uri.queryParameters},
       restorationId: state.pageKey.value,
-      child: child,
+      child: pageChild,
     );
   }
 
@@ -441,3 +449,21 @@ class _CustomNavigatorState extends State<_CustomNavigator> {
     );
   }
 }
+
+class _BranchNavigatorPopScope extends StatelessWidget {
+  const _BranchNavigatorPopScope({required this.navigatorActive, required this.child});
+
+  final ValueListenable<bool> navigatorActive;
+  final Widget child;
+
+  @override
+  Widget build(BuildContext context) {
+    return ValueListenableBuilder<bool>(
+      valueListenable: navigatorActive,
+      child: child,
+      builder: (BuildContext context, bool isActive, Widget? child) {
+        return PopScope<Object?>(canPop: isActive, child: child!);
+      },
+    );
+  }
+}
diff --git a/packages/go_router/lib/src/route.dart b/packages/go_router/lib/src/route.dart
index 6d75560a93cd..ae79bbdd603b 100644
--- a/packages/go_router/lib/src/route.dart
+++ b/packages/go_router/lib/src/route.dart
@@ -54,8 +54,9 @@ typedef NavigatorBuilder =
       ShellRouteMatch match,
       RouteMatchList matchList,
       List<NavigatorObserver>? observers,
-      String? restorationScopeId,
-    );
+      String? restorationScopeId, {
+      ValueListenable<bool>? navigatorActive,
+    });
 
 /// Signature for function used in [RouteBase.onExit].
 ///
@@ -566,8 +567,9 @@ class ShellRouteContext {
     BuildContext context,
     List<NavigatorObserver>? observers,
     bool notifyRootObserver,
-    String? restorationScopeId,
-  ) {
+    String? restorationScopeId, {
+    ValueListenable<bool>? navigatorActive,
+  }) {
     final effectiveObservers = <NavigatorObserver>[...?observers];
 
     if (notifyRootObserver) {
@@ -583,6 +585,7 @@ class ShellRouteContext {
       routeMatchList,
       effectiveObservers,
       restorationScopeId,
+      navigatorActive: navigatorActive,
     );
   }
 }
@@ -1375,12 +1378,21 @@ class StatefulNavigationShellState extends State<StatefulNavigationShell> with R
         branch.observers,
         route.notifyRootObserver,
         branch.restorationScopeId,
+        navigatorActive: branchState.navigatorActive,
       );
     }
+    _updateActiveBranchNavigatorFlags();
 
     _cleanUpObsoleteBranches();
   }
 
+  void _updateActiveBranchNavigatorFlags() {
+    for (var i = 0; i < route.branches.length; i++) {
+      final _StatefulShellBranchState? branchState = _branchState[route.branches[i]];
+      branchState?.navigatorActive.value = i == currentIndex;
+    }
+  }
+
   void _preloadBranches() {
     for (var i = 0; i < route.branches.length; i++) {
       final StatefulShellBranch branch = route.branches[i];
@@ -1398,15 +1410,17 @@ class StatefulNavigationShellState extends State<StatefulNavigationShell> with R
         });
         assert(match != null);
 
+        final _StatefulShellBranchState branchState = _branchStateFor(branch, false);
+        branchState.navigatorActive.value = false;
         final Widget navigator = widget.shellRouteContext.navigatorBuilder(
           branch.navigatorKey,
           match!,
           matchList,
           branch.observers,
           branch.restorationScopeId,
+          navigatorActive: branchState.navigatorActive,
         );
 
-        final _StatefulShellBranchState branchState = _branchStateFor(branch, false);
         branchState.location.value = matchList;
         branchState.navigator = navigator;
       }
@@ -1491,9 +1505,11 @@ class _StatefulShellBranchState {
 
   Widget? navigator;
   final _RestorableRouteMatchList location;
+  final ValueNotifier<bool> navigatorActive = ValueNotifier<bool>(false);
 
   void dispose() {
     location.dispose();
+    navigatorActive.dispose();
   }
 }
 
diff --git a/packages/go_router/pending_changelogs/change_2026_06_16_1781632636645.yaml b/packages/go_router/pending_changelogs/change_2026_06_16_1781632636645.yaml
new file mode 100644
index 000000000000..d96867104747
--- /dev/null
+++ b/packages/go_router/pending_changelogs/change_2026_06_16_1781632636645.yaml
@@ -0,0 +1,3 @@
+changelog: |
+  - Fixes Android system/predictive back popping inactive StatefulShellBranch navigators.
+version: patch
diff --git a/packages/go_router/test/stateful_shell_route_system_back_test.dart b/packages/go_router/test/stateful_shell_route_system_back_test.dart
index 7e66d58827a1..8389fe5fda4e 100644
--- a/packages/go_router/test/stateful_shell_route_system_back_test.dart
+++ b/packages/go_router/test/stateful_shell_route_system_back_test.dart
@@ -4,6 +4,7 @@
 
 import 'package:flutter/foundation.dart';
 import 'package:flutter/material.dart';
+import 'package:flutter/services.dart';
 import 'package:flutter_test/flutter_test.dart';
 import 'package:go_router/go_router.dart';
 
@@ -87,6 +88,93 @@ void main() {
       await tester.pumpAndSettle();
       expect(find.text('Home'), findsOneWidget);
     });
+
+    testWidgets('does not pop inactive StatefulShellRoute branches', (WidgetTester tester) async {
+      final pops = <String>[];
+      StatefulNavigationShell? navigationShell;
+      addTearDown(() async {
+        await tester.pumpWidget(const SizedBox.shrink());
+        await tester.pump();
+      });
+
+      final GoRouter router = await createRouter(
+        <RouteBase>[
+          StatefulShellRoute.indexedStack(
+            builder: (BuildContext context, GoRouterState state, StatefulNavigationShell shell) {
+              navigationShell = shell;
+              return shell;
+            },
+            branches: <StatefulShellBranch>[
+              StatefulShellBranch(
+                observers: <NavigatorObserver>[_RecordingNavigatorObserver('/A', pops)],
+                routes: <RouteBase>[
+                  GoRoute(
+                    path: '/A1',
+                    builder: (_, _) => const _BranchScreen(title: 'Stack A - 1', canPop: false),
+                    routes: <RouteBase>[
+                      GoRoute(
+                        path: '/A2',
+                        builder: (_, _) => const _BranchScreen(title: 'Stack A - 2'),
+                        routes: <RouteBase>[
+                          GoRoute(
+                            path: '/A3',
+                            builder: (_, _) => const _BranchScreen(title: 'Stack A - 3'),
+                          ),
+                        ],
+                      ),
+                    ],
+                  ),
+                ],
+              ),
+              StatefulShellBranch(
+                observers: <NavigatorObserver>[_RecordingNavigatorObserver('/B', pops)],
+                routes: <RouteBase>[
+                  GoRoute(
+                    path: '/B1',
+                    builder: (_, _) => const _BranchScreen(title: 'Stack B - 1', canPop: false),
+                  ),
+                ],
+              ),
+              StatefulShellBranch(
+                observers: <NavigatorObserver>[_RecordingNavigatorObserver('/C', pops)],
+                routes: <RouteBase>[
+                  GoRoute(
+                    path: '/C1',
+                    builder: (_, _) => const _BranchScreen(title: 'Stack C - 1', canPop: false),
+                    routes: <RouteBase>[
+                      GoRoute(
+                        path: '/C2',
+                        builder: (_, _) => const _BranchScreen(title: 'Stack C - 2'),
+                      ),
+                    ],
+                  ),
+                ],
+              ),
+            ],
+          ),
+        ],
+        tester,
+        initialLocation: '/A1',
+      );
+
+      router.go('/A1/A2/A3');
+      await tester.pumpAndSettle();
+      expect(find.text('Stack A - 3'), findsOneWidget);
+
+      router.go('/C1/C2');
+      await tester.pumpAndSettle();
+      expect(find.text('Stack C - 2'), findsOneWidget);
+
+      navigationShell!.goBranch(1);
+      await tester.pumpAndSettle();
+      expect(find.text('Stack B - 1'), findsOneWidget);
+
+      await simulateAndroidPredictiveBackGesture(tester);
+      await tester.pump();
+
+      expect(find.text('Stack B - 1'), findsOneWidget);
+      expect(pops, isEmpty);
+    });
   });
 }
 
@@ -172,3 +260,64 @@ class _TestAppState extends State<_TestApp> {
     return MaterialApp.router(routerConfig: _router);
   }
 }
+
+class _BranchScreen extends StatelessWidget {
+  const _BranchScreen({required this.title, this.canPop = true});
+
+  final String title;
+  final bool canPop;
+
+  @override
+  Widget build(BuildContext context) {
+    return PopScope<Object?>(
+      canPop: canPop,
+      child: Scaffold(body: Center(child: Text(title))),
+    );
+  }
+}
+
+class _RecordingNavigatorObserver extends NavigatorObserver {
+  _RecordingNavigatorObserver(this.branch, this.pops);
+
+  final String branch;
+  final List<String> pops;
+
+  @override
+  void didPop(Route<dynamic> route, Route<dynamic>? previousRoute) {
+    pops.add('$branch ${route.settings.name} -> ${previousRoute?.settings.name}');
+  }
+}
+
+Future<void> simulateAndroidPredictiveBackGesture(WidgetTester tester) async {
+  await _handleAndroidPredictiveBackMessage(
+    tester,
+    const MethodCall('startBackGesture', <String, dynamic>{
+      'touchOffset': <double>[5.0, 300.0],
+      'progress': 0.0,
+      'swipeEdge': 0,
+    }),
+  );
+  await tester.pump();
+
+  await _handleAndroidPredictiveBackMessage(
+    tester,
+    const MethodCall('updateBackGestureProgress', <String, dynamic>{
+      'x': 100.0,
+      'y': 300.0,
+      'progress': 0.35,
+      'swipeEdge': 0,
+    }),
+  );
+  await tester.pump();
+
+  await _handleAndroidPredictiveBackMessage(tester, const MethodCall('commitBackGesture'));
+}
+
+Future<void> _handleAndroidPredictiveBackMessage(WidgetTester tester, MethodCall methodCall) async {
+  final ByteData message = const StandardMethodCodec().encodeMethodCall(methodCall);
+  await tester.binding.defaultBinaryMessenger.handlePlatformMessage(
+    'flutter/backgesture',
+    message,
+    (ByteData? _) {},
+  );
+}