diff --git a/server/coordinator_test.go b/server/coordinator_test.go
index 3dc3d376ef0..b9d31765e0a 100644
--- a/server/coordinator_test.go
+++ b/server/coordinator_test.go
@@ -508,6 +508,53 @@ func (s *testCoordinatorSuite) TestShouldRun(c *C) {
 	c.Assert(co.cluster.prepareChecker.sum, Equals, 7)
 
 }
+func (s *testCoordinatorSuite) TestShouldRunWithNonLeaderRegions(c *C) {
+	_, opt, err := newTestScheduleConfig()
+	c.Assert(err, IsNil)
+	tc := newTestClusterInfo(opt)
+	hbStreams := newHeartbeatStreams(tc.getClusterID())
+	defer hbStreams.Close()
+
+	co := newCoordinator(tc.clusterInfo, hbStreams, namespace.DefaultClassifier)
+
+	c.Assert(tc.addLeaderStore(1, 10), IsNil)
+	c.Assert(tc.addLeaderStore(2, 0), IsNil)
+	c.Assert(tc.addLeaderStore(3, 0), IsNil)
+	for i := 0; i < 10; i++ {
+		c.Assert(tc.LoadRegion(uint64(i+1), 1, 2, 3), IsNil)
+	}
+	c.Assert(co.shouldRun(), IsFalse)
+	c.Assert(tc.core.Regions.GetStoreRegionCount(1), Equals, 10)
+
+	tbl := []struct {
+		regionID  uint64
+		shouldRun bool
+	}{
+		{1, false},
+		{2, false},
+		{3, false},
+		{4, false},
+		{5, false},
+		{6, false},
+		{7, false},
+		{8, true},
+	}
+
+	for _, t := range tbl {
+		r := tc.GetRegion(t.regionID)
+		nr := r.Clone(core.WithLeader(r.GetPeers()[0]))
+		c.Assert(tc.handleRegionHeartbeat(nr), IsNil)
+		c.Assert(co.shouldRun(), Equals, t.shouldRun)
+	}
+	nr := &metapb.Region{Id: 8, Peers: []*metapb.Peer{}}
+	newRegion := core.NewRegionInfo(nr, nil)
+	c.Assert(tc.handleRegionHeartbeat(newRegion), NotNil)
+	c.Assert(co.cluster.prepareChecker.sum, Equals, 8)
+
+	// Now, after server is prepared, there exist some regions with no leader.
+	c.Assert(tc.GetRegion(9).GetLeader().GetStoreId(), Equals, uint64(0))
+	c.Assert(tc.GetRegion(10).GetLeader().GetStoreId(), Equals, uint64(0))
+}
 
 func (s *testCoordinatorSuite) TestAddScheduler(c *C) {
 	cfg, opt, err := newTestScheduleConfig()
diff --git a/server/schedule/range_cluster.go b/server/schedule/range_cluster.go
index cdb924141d9..e4db455c9e1 100644
--- a/server/schedule/range_cluster.go
+++ b/server/schedule/range_cluster.go
@@ -91,7 +91,9 @@ func (r *RangeCluster) updateStoreInfo(s *core.StoreInfo) *core.StoreInfo {
 // GetStore searches for a store by ID.
 func (r *RangeCluster) GetStore(id uint64) *core.StoreInfo {
 	s := r.Cluster.GetStore(id)
-	r.updateStoreInfo(s)
+	if s != nil {
+		r.updateStoreInfo(s)
+	}
 	return s
 }
 
@@ -154,6 +156,8 @@ func (r *RangeCluster) GetFollowerStores(region *core.RegionInfo) []*core.StoreI
 // GetLeaderStore returns all stores that contains the region's leader peer.
 func (r *RangeCluster) GetLeaderStore(region *core.RegionInfo) *core.StoreInfo {
 	s := r.Cluster.GetLeaderStore(region)
-	r.updateStoreInfo(s)
+	if s != nil {
+		r.updateStoreInfo(s)
+	}
 	return s
 }
diff --git a/server/schedulers/balance_test.go b/server/schedulers/balance_test.go
index 882f03db60b..e6846115f0d 100644
--- a/server/schedulers/balance_test.go
+++ b/server/schedulers/balance_test.go
@@ -1306,3 +1306,69 @@ func (s *testScatterRangeLeaderSuite) TestBalance(c *C) {
 		c.Check(regionCount, LessEqual, 32)
 	}
 }
+
+func (s *testScatterRangeLeaderSuite) TestBalanceWhenRegionNotHeartbeat(c *C) {
+	opt := schedule.NewMockSchedulerOptions()
+	tc := schedule.NewMockCluster(opt)
+	// Add stores 1,2,3.
+	tc.AddRegionStore(1, 0)
+	tc.AddRegionStore(2, 0)
+	tc.AddRegionStore(3, 0)
+	var (
+		id      uint64
+		regions []*metapb.Region
+	)
+	for i := 0; i < 10; i++ {
+		peers := []*metapb.Peer{
+			{Id: id + 1, StoreId: 1},
+			{Id: id + 2, StoreId: 2},
+			{Id: id + 3, StoreId: 3},
+		}
+		regions = append(regions, &metapb.Region{
+			Id:       id + 4,
+			Peers:    peers,
+			StartKey: []byte(fmt.Sprintf("s_%02d", i)),
+			EndKey:   []byte(fmt.Sprintf("s_%02d", i+1)),
+		})
+		id += 4
+	}
+	// empty case
+	regions[9].EndKey = []byte("")
+
+	// To simulate server prepared,
+	// store 1 contains 8 leader region peers and leaders of 2 regions are unknown yet.
+	for _, meta := range regions {
+		var leader *metapb.Peer
+		if meta.Id < 8 {
+			leader = meta.Peers[0]
+		}
+		regionInfo := core.NewRegionInfo(
+			meta,
+			leader,
+			core.SetApproximateKeys(96),
+			core.SetApproximateSize(96),
+		)
+
+		tc.Regions.SetRegion(regionInfo)
+	}
+
+	for i := 1; i <= 3; i++ {
+		tc.UpdateStoreStatus(uint64(i))
+	}
+
+	oc := schedule.NewOperatorController(nil, nil)
+	hb := newScatterRangeScheduler(oc, []string{"s_00", "s_09", "t"})
+
+	limit := 0
+	for {
+		if limit > 100 {
+			break
+		}
+		ops := hb.Schedule(tc)
+		if ops == nil {
+			limit++
+			continue
+		}
+		tc.ApplyOperator(ops[0])
+	}
+}