diff --git a/pkgs/jnigen/lib/src/config/yaml_reader.dart b/pkgs/jnigen/lib/src/config/yaml_reader.dart
index c9b77de1d3..aacf24ff12 100644
--- a/pkgs/jnigen/lib/src/config/yaml_reader.dart
+++ b/pkgs/jnigen/lib/src/config/yaml_reader.dart
@@ -88,17 +88,55 @@ class YamlReader {
   /// from YAML config.
   Uri? getPath(String property) => _config.optionalPath(property);
 
-  List<String>? getStringList(String property) => _config.optionalStringList(
-        property,
-        splitCliPattern: ';',
-        combineAllConfigs: false,
-      );
-
-  List<Uri>? getPathList(String property) => _config.optionalPathList(
-        property,
-        combineAllConfigs: false,
-        splitCliPattern: ';',
-      );
+  /// Reports an entry left empty in [property], which reads as null.
+  ///
+  /// A list read from the config file is cast lazily, so such an entry only
+  /// fails where something reaches for it, with a message that names neither
+  /// the property nor the file. A list that came from `-D` holds its own
+  /// strings and cannot carry a null.
+  ///
+  /// Pass the list through `cast<Object?>()`: reading an element of the cast
+  /// list throws before this can see it, and casting again unwraps to the
+  /// source rather than stacking on top of it.
+  void _checkForEmptyEntries(String property, List<Object?> values) {
+    for (var i = 0; i < values.length; ++i) {
+      if (values[i] == null) {
+        throw ConfigException(
+            'Entry ${i + 1} of "$property" is empty in the config file.');
+      }
+    }
+  }
+
+  List<String>? getStringList(String property) {
+    final values = _config.optionalStringList(
+      property,
+      splitCliPattern: ';',
+      combineAllConfigs: false,
+    );
+    if (values == null) return null;
+    // The cast is what lets the check read a null; see the helper.
+    _checkForEmptyEntries(property, values.cast<Object?>());
+    return values;
+  }
+
+  List<Uri>? getPathList(String property) {
+    // `optionalPathList` reads the entries itself, so they have to be checked
+    // before it does.
+    final values = _config.optionalStringList(
+      property,
+      splitCliPattern: ';',
+      combineAllConfigs: false,
+    );
+    if (values != null) {
+      // The cast is what lets the check read a null; see the helper.
+      _checkForEmptyEntries(property, values.cast<Object?>());
+    }
+    return _config.optionalPathList(
+      property,
+      combineAllConfigs: false,
+      splitCliPattern: ';',
+    );
+  }
 
   String? getOneOf(String property, Set<String> values) =>
       _config.optionalString(property, validValues: values);
diff --git a/pkgs/jnigen/test/config_test.dart b/pkgs/jnigen/test/config_test.dart
index f87c9d12d7..30a5634ed7 100644
--- a/pkgs/jnigen/test/config_test.dart
+++ b/pkgs/jnigen/test/config_test.dart
@@ -123,5 +123,26 @@ void main() async {
       name: 'Nested class specified',
       overrides: ['-Dclasses=com.android.Clock\$Clock'],
     );
+
+    for (final property in ['classes', 'source_path']) {
+      test('Empty entry in $property', () {
+        // Not expressible as an override: the -D parser requires a value.
+        final dir = Directory.systemTemp.createTempSync('jnigen_config_test');
+        addTearDown(() => dir.deleteSync(recursive: true));
+        final yaml = File(join(dir.path, 'jnigen.yaml'))..writeAsStringSync('''
+output:
+  dart:
+    path: lib/gen.dart
+    structure: single_file
+$property:
+  - "com.example.Foo"
+  -
+${property == 'classes' ? '' : 'classes:\n  - "com.example.Foo"\n'}''');
+        expect(
+          () => Config.parseArgs(['--config', yaml.path]),
+          throwsA(isA<ConfigException>()),
+        );
+      });
+    }
   });
 }