diff --git a/services/pull/pull.go b/services/pull/pull.go
index c3c9b9f9303..0b753e46890 100644
--- a/services/pull/pull.go
+++ b/services/pull/pull.go
@@ -475,7 +475,7 @@ func CloseBranchPulls(doer *models.User, repoID int64, branch string) error {
 	return nil
 }
 
-// CloseRepoBranchesPulls close all pull requests which head branches are in the given repository
+// CloseRepoBranchesPulls close all pull requests which head branches are in the given repository, but only whose base repo is not in the given repository
 func CloseRepoBranchesPulls(doer *models.User, repo *models.Repository) error {
 	branches, err := git.GetBranchesByPath(repo.RepoPath())
 	if err != nil {
@@ -494,6 +494,11 @@ func CloseRepoBranchesPulls(doer *models.User, repo *models.Repository) error {
 		}
 
 		for _, pr := range prs {
+			// If the base repository for this pr is this repository there is no need to close it
+			// as it is going to be deleted anyway
+			if pr.BaseRepoID == repo.ID {
+				continue
+			}
 			if err = issue_service.ChangeStatus(pr.Issue, doer, true); err != nil && !models.IsErrPullWasClosed(err) {
 				errs = append(errs, err)
 			}