diff --git a/source/source_github.go b/source/source_github.go
index 80550d8..6db0de0 100644
--- a/source/source_github.go
+++ b/source/source_github.go
@@ -139,6 +139,11 @@ func (s SourceGitHub) Load(ctx context.Context, logger kitlog.Logger) ([]*Source
 					"owner", target.Owner, "repo", target.Repo, "ref", target.Ref)
 				tree, _, err := client.Git.GetTree(ctx, target.Owner, target.Repo, target.Ref, true)
 				if err != nil {
+					if repositoryEmpty(err) {
+						logger.Log("msg", "GitHub repository is empty, skipping",
+							"owner", target.Owner, "repo", target.Repo, "ref", target.Ref)
+						return nil
+					}
 					return errors.Wrap(err, fmt.Sprintf("getting tree for '%s/%s' at ref %s", target.Owner, target.Repo, target.Ref))
 				}
 
@@ -222,3 +227,10 @@ func (s SourceGitHub) Load(ctx context.Context, logger kitlog.Logger) ([]*Source
 
 	return entries, nil
 }
+
+func repositoryEmpty(err error) bool {
+	if err == nil {
+		return false
+	}
+	return strings.Contains(err.Error(), "409 Git Repository is empty")
+}