diff --git a/tools/engine_tool/lib/src/commands/query_command.dart b/tools/engine_tool/lib/src/commands/query_command.dart
index 37ed01031a290..c22f61803047e 100644
--- a/tools/engine_tool/lib/src/commands/query_command.dart
+++ b/tools/engine_tool/lib/src/commands/query_command.dart
@@ -221,7 +221,8 @@ et query targets //flutter/fml/...  # List all targets under `//flutter/fml`
     }
 
     if (allTargets.isEmpty) {
-      environment.logger.fatal('Query unexpectedly returned an empty list');
+      environment.logger.error('No targets found, nothing to query.');
+      return 1;
     }
 
     for (final BuildTarget target in allTargets) {
diff --git a/tools/engine_tool/lib/src/commands/test_command.dart b/tools/engine_tool/lib/src/commands/test_command.dart
index a48e10efec093..3c3b656774851 100644
--- a/tools/engine_tool/lib/src/commands/test_command.dart
+++ b/tools/engine_tool/lib/src/commands/test_command.dart
@@ -86,6 +86,11 @@ et test //flutter/fml:fml_benchmarks  # Run a single test target in `//flutter/f
       buildTargets.addAll(found);
     }
 
+    if (buildTargets.isEmpty) {
+      environment.logger.error('No targets found, nothing to test.');
+      return 1;
+    }
+
     // Make sure there is at least one test target.
     final List<ExecutableBuildTarget> testTargets = buildTargets
         .whereType<ExecutableBuildTarget>()
diff --git a/tools/engine_tool/lib/src/gn.dart b/tools/engine_tool/lib/src/gn.dart
index a1a29bbcd16ab..d203ee685af80 100644
--- a/tools/engine_tool/lib/src/gn.dart
+++ b/tools/engine_tool/lib/src/gn.dart
@@ -55,6 +55,26 @@ interface class Gn {
       failOk: true,
     );
     if (process.exitCode != 0) {
+      // If the error was in the format:
+      // "The input testing/scenario_app:scenario_app matches no targets, configs or files."
+      //
+      // Then report a nicer error, versus a fatal error.
+      final stdout = process.stdout;
+      if (stdout.contains('matches no targets, configs or files')) {
+        final gnPattern = pattern.toGnPattern();
+        if (!gnPattern.startsWith('//flutter')) {
+          _environment.logger.warning(
+            'No targets matched the pattern `$gnPattern`.'
+            'Did you mean `//flutter/$gnPattern`?',
+          );
+        } else {
+          _environment.logger.warning(
+            'No targets matched the pattern `${pattern.toGnPattern()}`',
+          );
+        }
+        return <BuildTarget>[];
+      }
+
       _environment.logger.fatal(
         'Failed to run `${command.join(' ')}` (exit code ${process.exitCode})'
         '\n\n'
diff --git a/tools/engine_tool/test/build_command_test.dart b/tools/engine_tool/test/build_command_test.dart
index c8af8cc3fe68a..1344db1053b49 100644
--- a/tools/engine_tool/test/build_command_test.dart
+++ b/tools/engine_tool/test/build_command_test.dart
@@ -424,6 +424,36 @@ void main() {
     }
   });
 
+  test('build command gracefully handles no matched targets', () async {
+    final List<CannedProcess> cannedProcesses = <CannedProcess>[
+      CannedProcess((List<String> command) =>
+          command.contains('desc'),
+          stdout: fixtures.gnDescOutputEmpty(gnPattern: 'testing/scenario_app:sceario_app'),
+          exitCode: 1),
+    ];
+    final TestEnvironment testEnv = TestEnvironment.withTestEngine(
+      cannedProcesses: cannedProcesses,
+    );
+    try {
+      final ToolCommandRunner runner = ToolCommandRunner(
+        environment: testEnv.environment,
+        configs: configs,
+      );
+      final int result = await runner.run(<String>[
+        'build',
+        '--config',
+        'host_debug',
+        // Intentionally omit the prefix '//flutter/' to trigger the warning.
+        '//testing/scenario_app',
+      ]);
+      expect(result, equals(0));
+      expect(testEnv.testLogs.map((LogRecord r) => r.message).join(),
+          contains('No targets matched the pattern `testing/scenario_app'));
+    } finally {
+      testEnv.cleanup();
+    }
+  });
+
   test('et help build line length is not too big', () async {
     final List<String> prints = <String>[];
     await runZoned(
diff --git a/tools/engine_tool/test/fixtures.dart b/tools/engine_tool/test/fixtures.dart
index b31b24b58b688..70de4d36a94ba 100644
--- a/tools/engine_tool/test/fixtures.dart
+++ b/tools/engine_tool/test/fixtures.dart
@@ -319,3 +319,7 @@ String gnDescOutput() => '''
    }
 }
 ''';
+
+String gnDescOutputEmpty({required String gnPattern}) => '''
+The input $gnPattern matches no targets, configs or files.
+''';