diff --git a/models/migrations/migrations.go b/models/migrations/migrations.go
index ce3f77ba4..794074524 100644
--- a/models/migrations/migrations.go
+++ b/models/migrations/migrations.go
@@ -188,6 +188,8 @@ var migrations = []Migration{
 	NewMigration("Fix topic repository count", fixTopicRepositoryCount),
 	// v127 -> v128
 	NewMigration("add repository code language statistics", addLanguageStats),
+	// v128 -> v129
+	NewMigration("fix merge base for pull requests", fixMergeBase),
 }
 
 // Migrate database to current version
diff --git a/models/migrations/v128.go b/models/migrations/v128.go
new file mode 100644
index 000000000..557282bf2
--- /dev/null
+++ b/models/migrations/v128.go
@@ -0,0 +1,97 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package migrations
+
+import (
+	"fmt"
+	"path/filepath"
+	"strings"
+
+	"code.gitea.io/gitea/modules/git"
+	"code.gitea.io/gitea/modules/log"
+	"code.gitea.io/gitea/modules/setting"
+
+	"xorm.io/xorm"
+)
+
+func fixMergeBase(x *xorm.Engine) error {
+	type Repository struct {
+		ID        int64 `xorm:"pk autoincr"`
+		OwnerID   int64 `xorm:"UNIQUE(s) index"`
+		OwnerName string
+		LowerName string `xorm:"UNIQUE(s) INDEX NOT NULL"`
+		Name      string `xorm:"INDEX NOT NULL"`
+	}
+
+	type PullRequest struct {
+		ID         int64 `xorm:"pk autoincr"`
+		Index      int64
+		HeadRepoID int64 `xorm:"INDEX"`
+		BaseRepoID int64 `xorm:"INDEX"`
+		HeadBranch string
+		BaseBranch string
+		MergeBase  string `xorm:"VARCHAR(40)"`
+
+		HasMerged      bool   `xorm:"INDEX"`
+		MergedCommitID string `xorm:"VARCHAR(40)"`
+	}
+
+	var limit = setting.Database.IterateBufferSize
+	if limit <= 0 {
+		limit = 50
+	}
+
+	i := 0
+	for {
+		prs := make([]PullRequest, 0, 50)
+		if err := x.Limit(limit, i).Asc("id").Find(&prs); err != nil {
+			return fmt.Errorf("Find: %v", err)
+		}
+		if len(prs) == 0 {
+			break
+		}
+
+		i += 50
+		for _, pr := range prs {
+			baseRepo := &Repository{ID: pr.BaseRepoID}
+			has, err := x.Table("repository").Get(baseRepo)
+			if err != nil {
+				return fmt.Errorf("Unable to get base repo %d %v", pr.BaseRepoID, err)
+			}
+			if !has {
+				log.Error("Missing base repo with id %d for PR ID %d", pr.BaseRepoID, pr.ID)
+				continue
+			}
+			userPath := filepath.Join(setting.RepoRootPath, strings.ToLower(baseRepo.OwnerName))
+			repoPath := filepath.Join(userPath, strings.ToLower(baseRepo.Name)+".git")
+
+			gitRefName := fmt.Sprintf("refs/pull/%d/head", pr.Index)
+
+			if !pr.HasMerged {
+				var err error
+				pr.MergeBase, err = git.NewCommand("merge-base", "--", pr.BaseBranch, gitRefName).RunInDir(repoPath)
+				if err != nil {
+					var err2 error
+					pr.MergeBase, err2 = git.NewCommand("rev-parse", git.BranchPrefix+pr.BaseBranch).RunInDir(repoPath)
+					if err2 != nil {
+						log.Error("Unable to get merge base for PR ID %d, Index %d in %s/%s. Error: %v & %v", pr.ID, pr.Index, baseRepo.OwnerName, baseRepo.Name, err, err2)
+						continue
+					}
+				}
+			} else {
+				var err error
+				pr.MergeBase, err = git.NewCommand("merge-base", "--", pr.MergedCommitID+"^", gitRefName).RunInDir(repoPath)
+				if err != nil {
+					log.Error("Unable to get merge base for merged PR ID %d, Index %d in %s/%s. Error: %", pr.ID, pr.Index, baseRepo.OwnerName, baseRepo.Name, err)
+					continue
+				}
+			}
+			pr.MergeBase = strings.TrimSpace(pr.MergeBase)
+			x.ID(pr.ID).Cols("merge_base").Update(pr)
+		}
+	}
+
+	return nil
+}