diff --git a/lib/manager/gitlabci-include/extract.ts b/lib/manager/gitlabci-include/extract.ts
index 654f5db8efafafa9f6bdeafcb9d9eaf64be11a1b..c56c6735d0a56cade7c61108fd4727d6b82cdcf2 100644
--- a/lib/manager/gitlabci-include/extract.ts
+++ b/lib/manager/gitlabci-include/extract.ts
@@ -48,8 +48,7 @@ export function extractPackageFile(
     }
   } catch (err) /* istanbul ignore next */ {
     if (err.stack?.startsWith('YAMLException:')) {
-      logger.debug({ err });
-      logger.debug('YAML exception extracting GitLab CI includes');
+      logger.debug({ err }, 'YAML exception extracting GitLab CI includes');
     } else {
       logger.warn({ err }, 'Error extracting GitLab CI includes');
     }
diff --git a/lib/manager/gitlabci/__fixtures__/gitlab-ci.3.yaml b/lib/manager/gitlabci/__fixtures__/gitlab-ci.3.yaml
index afd94b368ebad08d8e7c4092b87553127b2c7acb..3394b4009976f9c481ae447a7bbc41d8081d276e 100644
--- a/lib/manager/gitlabci/__fixtures__/gitlab-ci.3.yaml
+++ b/lib/manager/gitlabci/__fixtures__/gitlab-ci.3.yaml
@@ -12,6 +12,7 @@ include:
   - local: 'lib/manager/gitlabci/__fixtures__/include.yml'
   - local: 'lib/manager/gitlabci/__fixtures__/include.yml' # Loop detection
   - local: 'lib/manager/gitlabci/__fixtures__/include.1.yml'
+  - local: 'lib/manager/gitlabci/__fixtures__/*/.gitlab-ci.yml'
   - project: 'my-group/my-project'
     ref: master
     file: '/templates/.gitlab-ci-template.yml'
diff --git a/lib/manager/gitlabci/extract.ts b/lib/manager/gitlabci/extract.ts
index 0576720769737a9828f7acf567bb515f0619c960..7ef26896f205cb9de3335c50bd4aa4d1bbf01937 100644
--- a/lib/manager/gitlabci/extract.ts
+++ b/lib/manager/gitlabci/extract.ts
@@ -99,6 +99,11 @@ export async function extractAllPackageFiles(
     const file = filesToExamine.pop();
 
     const content = await readLocalFile(file, 'utf8');
+    if (!content) {
+      logger.debug({ file }, 'Empty or non existent gitlabci file');
+      // eslint-disable-next-line no-continue
+      continue;
+    }
     let doc: GitlabPipeline;
     try {
       doc = yaml.safeLoad(replaceReferenceTags(content), {