diff --git a/js.go b/js.go
index 4d4adbdac..626fcabfd 100644
--- a/js.go
+++ b/js.go
@@ -94,6 +94,14 @@ const (
 
 	// Scale for threshold of missed HBs or lack of activity.
 	hbcThresh = 2
+
+	// For ChanSubscription, we can't update sub.delivered as we do for other
+	// type of subscriptions, since the channel is user provided.
+	// With flow control in play, we will check for flow control on incoming
+	// messages (as opposed to when they are delivered), but also from a go
+	// routine. Without this, the subscription would possibly stall until
+	// a new message or heartbeat/fc are received.
+	chanSubFCCheckInterval = 250 * time.Millisecond
 )
 
 // Types of control messages, so far heartbeat and flow control
@@ -897,6 +905,8 @@ type jsSub struct {
 	cmeta  string
 	fcr    string
 	fcd    uint64
+	fciseq uint64
+	csfct  *time.Timer
 }
 
 // Deletes the JS Consumer.
@@ -1409,15 +1419,27 @@ func (js *js) subscribe(subj, queue string, cb MsgHandler, ch chan *Msg, isSync,
 				}
 				if !isPullMode {
 					// We can't reuse the channel, so if one was passed, we need to create a new one.
-					if ch != nil {
+					if isSync {
 						ch = make(chan *Msg, cap(ch))
+					} else if ch != nil {
+						// User provided (ChanSubscription), simply try to drain it.
+						for done := false; !done; {
+							select {
+							case <-ch:
+							default:
+								done = true
+							}
+						}
 					}
 					jsi.deliver = deliver
+					jsi.hbi = info.Config.Heartbeat
 					// Recreate the subscription here.
 					sub, err = nc.subscribe(jsi.deliver, queue, cb, ch, isSync, jsi)
 					if err != nil {
 						return nil, err
 					}
+					hasFC = info.Config.FlowControl
+					hasHeartbeats = info.Config.Heartbeat > 0
 				}
 			} else {
 				if cinfo.Error.Code == 404 {
@@ -1442,10 +1464,44 @@ func (js *js) subscribe(subj, queue string, cb MsgHandler, ch chan *Msg, isSync,
 	if hasHeartbeats {
 		sub.scheduleHeartbeatCheck()
 	}
+	// For ChanSubscriptions, if we know that there is flow control, we will
+	// start a go routine that evaluates the number of delivered messages
+	// and process flow control.
+	if sub.Type() == ChanSubscription && hasFC {
+		sub.chanSubcheckForFlowControlResponse()
+	}
 
 	return sub, nil
 }
 
+// This long-lived routine is used per ChanSubscription to check
+// on the number of delivered messages and check for flow control response.
+func (sub *Subscription) chanSubcheckForFlowControlResponse() {
+	sub.mu.Lock()
+	// We don't use defer since if we need to send an RC reply, we need
+	// to do it outside the sub's lock. So doing explicit unlock...
+	if sub.closed {
+		sub.mu.Unlock()
+		return
+	}
+	var fcReply string
+	var nc *Conn
+
+	jsi := sub.jsi
+	if jsi.csfct == nil {
+		jsi.csfct = time.AfterFunc(chanSubFCCheckInterval, sub.chanSubcheckForFlowControlResponse)
+	} else {
+		fcReply = sub.checkForFlowControlResponse()
+		nc = sub.conn
+		// Do the reset here under the lock, it's ok...
+		jsi.csfct.Reset(chanSubFCCheckInterval)
+	}
+	sub.mu.Unlock()
+	// This call will return an error (which we don't care here)
+	// if nc is nil or fcReply is empty.
+	nc.Publish(fcReply, nil)
+}
+
 // ErrConsumerSequenceMismatch represents an error from a consumer
 // that received a Heartbeat including sequence different to the
 // one expected from the view of the client.
@@ -1488,8 +1544,11 @@ func isJSControlMessage(msg *Msg) (bool, int) {
 
 // Keeps track of the incoming message's reply subject so that the consumer's
 // state (deliver sequence, etc..) can be checked against heartbeats.
+// We will also bump the incoming data message sequence that is used in FC cases.
 // Runs under the subscription lock
 func (sub *Subscription) trackSequences(reply string) {
+	// For flow control, keep track of incoming message sequence.
+	sub.jsi.fciseq++
 	sub.jsi.cmeta = reply
 }
 
@@ -1626,13 +1685,25 @@ func (sub *Subscription) resetOrderedConsumer(sseq uint64) {
 	}()
 }
 
+// For jetstream subscriptions, returns the number of delivered messages.
+// For ChanSubscription, this value is computed based on the known number
+// of messages added to the channel minus the current size of that channel.
+// Lock held on entry
+func (sub *Subscription) getJSDelivered() uint64 {
+	if sub.typ == ChanSubscription {
+		return sub.jsi.fciseq - uint64(len(sub.mch))
+	}
+	return sub.delivered
+}
+
 // checkForFlowControlResponse will check to see if we should send a flow control response
 // based on the subscription current delivered index and the target.
 // Runs under subscription lock
 func (sub *Subscription) checkForFlowControlResponse() string {
 	// Caller has verified that there is a sub.jsi and fc
 	jsi := sub.jsi
-	if jsi.fcd == sub.delivered {
+	jsi.active = true
+	if sub.getJSDelivered() >= jsi.fcd {
 		fcr := jsi.fcr
 		jsi.fcr, jsi.fcd = _EMPTY_, 0
 		return fcr
@@ -1642,9 +1713,8 @@ func (sub *Subscription) checkForFlowControlResponse() string {
 
 // Record an inbound flow control message.
 // Runs under subscription lock
-func (sub *Subscription) scheduleFlowControlResponse(dfuture uint64, reply string) {
-	jsi := sub.jsi
-	jsi.fcr, jsi.fcd = reply, dfuture
+func (sub *Subscription) scheduleFlowControlResponse(reply string) {
+	sub.jsi.fcr, sub.jsi.fcd = reply, sub.jsi.fciseq
 }
 
 // Checks for activity from our consumer.
diff --git a/js_test.go b/js_test.go
index 90c03fe64..9685ce154 100644
--- a/js_test.go
+++ b/js_test.go
@@ -105,7 +105,10 @@ func TestJetStreamOrderedConsumer(t *testing.T) {
 		} else {
 			chunk = msg[i : i+chunkSize]
 		}
-		js.PublishAsync("a", chunk)
+		msg := NewMsg("a")
+		msg.Data = chunk
+		msg.Header.Set("data", "true")
+		js.PublishMsgAsync(msg)
 	}
 	js.PublishAsync("a", nil) // eof
 
@@ -171,7 +174,7 @@ func TestJetStreamOrderedConsumer(t *testing.T) {
 				t.Fatalf("Objects do not match")
 			}
 		case <-time.After(5 * time.Second):
-			t.Fatalf("Did not receive all chunks, only %d of %d total", atomic.LoadUint32(&received), si.State.Msgs)
+			t.Fatalf("Did not receive all chunks, only %d of %d total", atomic.LoadUint32(&received), si.State.Msgs-1)
 		}
 	}
 
@@ -202,7 +205,7 @@ func TestJetStreamOrderedConsumer(t *testing.T) {
 			rmsg = append(rmsg, m.Data...)
 		}
 		if !done {
-			t.Fatalf("Did not receive all chunks, only %d of %d total", received, si.State.Msgs)
+			t.Fatalf("Did not receive all chunks, only %d of %d total", received, si.State.Msgs-1)
 		}
 		if rsum := sha256.Sum256(rmsg); rsum != sum {
 			t.Fatalf("Objects do not match")
@@ -215,7 +218,7 @@ func TestJetStreamOrderedConsumer(t *testing.T) {
 
 	// Now introduce some loss.
 	singleLoss := func(m *Msg) *Msg {
-		if rand.Intn(100) <= 10 {
+		if rand.Intn(100) <= 10 && m.Header.Get("data") != _EMPTY_ {
 			nc.removeMsgFilter("a")
 			return nil
 		}
@@ -223,10 +226,11 @@ func TestJetStreamOrderedConsumer(t *testing.T) {
 	}
 	nc.addMsgFilter("a", singleLoss)
 	testConsumer()
+	nc.addMsgFilter("a", singleLoss)
 	testSyncConsumer()
 
 	multiLoss := func(m *Msg) *Msg {
-		if rand.Intn(100) <= 10 {
+		if rand.Intn(100) <= 10 && m.Header.Get("data") != _EMPTY_ {
 			return nil
 		}
 		return m
@@ -246,11 +250,12 @@ func TestJetStreamOrderedConsumer(t *testing.T) {
 	}
 	nc.addMsgFilter("a", firstOnly)
 	testConsumer()
+	nc.addMsgFilter("a", firstOnly)
 	testSyncConsumer()
 
 	lastOnly := func(m *Msg) *Msg {
 		if meta, err := m.Metadata(); err == nil {
-			if meta.Sequence.Stream >= si.State.LastSeq {
+			if meta.Sequence.Stream >= si.State.LastSeq-1 {
 				nc.removeMsgFilter("a")
 				return nil
 			}
@@ -259,6 +264,7 @@ func TestJetStreamOrderedConsumer(t *testing.T) {
 	}
 	nc.addMsgFilter("a", lastOnly)
 	testConsumer()
+	nc.addMsgFilter("a", lastOnly)
 	testSyncConsumer()
 }
 
diff --git a/nats.go b/nats.go
index ed8506eb2..95a5577df 100644
--- a/nats.go
+++ b/nats.go
@@ -2600,7 +2600,6 @@ func (nc *Conn) waitForMsgs(s *Subscription) {
 			delivered = s.delivered
 			if s.jsi != nil {
 				fcReply = s.checkForFlowControlResponse()
-				s.jsi.active = true
 			}
 		}
 		s.mu.Unlock()
@@ -2768,6 +2767,7 @@ func (nc *Conn) processMsg(data []byte) {
 
 	// Skip processing if this is a control message.
 	if !ctrlMsg {
+		var chanSubCheckFC bool
 		// Subscription internal stats (applicable only for non ChanSubscription's)
 		if sub.typ != ChanSubscription {
 			sub.pMsgs++
@@ -2784,6 +2784,8 @@ func (nc *Conn) processMsg(data []byte) {
 				(sub.pBytesLimit > 0 && sub.pBytes > sub.pBytesLimit) {
 				goto slowConsumer
 			}
+		} else if jsi != nil {
+			chanSubCheckFC = true
 		}
 
 		// We have two modes of delivery. One is the channel, used by channel
@@ -2811,15 +2813,26 @@ func (nc *Conn) processMsg(data []byte) {
 			// Store the ACK metadata from the message to
 			// compare later on with the received heartbeat.
 			sub.trackSequences(m.Reply)
+			if chanSubCheckFC {
+				// For ChanSubscription, since we can't call this when a message
+				// is "delivered" (since user is pull from their own channel),
+				// we have a go routine that does this check, however, we do it
+				// also here to make it much more responsive. The go routine is
+				// really to avoid stalling when there is no new messages coming.
+				fcReply = sub.checkForFlowControlResponse()
+			}
 		}
 	} else if ctrlType == jsCtrlFC && m.Reply != _EMPTY_ {
 		// This is a flow control message.
-		// If we have no pending, go ahead and send in place.
-		if sub.pMsgs <= 0 {
+		// We will schedule the send of the FC reply once we have delivered the
+		// DATA message that was received before this flow control message, which
+		// has sequence `jsi.fciseq`. However, it is possible that this message
+		// has already been delivered, in that case, we need to send the FC reply now.
+		if sub.getJSDelivered() >= jsi.fciseq {
 			fcReply = m.Reply
 		} else {
 			// Schedule a reply after the previous message is delivered.
-			sub.scheduleFlowControlResponse(sub.delivered+uint64(sub.pMsgs), m.Reply)
+			sub.scheduleFlowControlResponse(m.Reply)
 		}
 	}
 
@@ -3851,9 +3864,15 @@ func (nc *Conn) removeSub(s *Subscription) {
 	s.mch = nil
 
 	// If JS subscription then stop HB timer.
-	if jsi := s.jsi; jsi != nil && jsi.hbc != nil {
-		jsi.hbc.Stop()
-		jsi.hbc = nil
+	if jsi := s.jsi; jsi != nil {
+		if jsi.hbc != nil {
+			jsi.hbc.Stop()
+			jsi.hbc = nil
+		}
+		if jsi.csfct != nil {
+			jsi.csfct.Stop()
+			jsi.csfct = nil
+		}
 	}
 
 	// Mark as invalid
@@ -4192,7 +4211,6 @@ func (s *Subscription) processNextMsgDelivered(msg *Msg) error {
 	delivered := s.delivered
 	if s.jsi != nil {
 		fcReply = s.checkForFlowControlResponse()
-		s.jsi.active = true
 	}
 
 	if s.typ == SyncSubscription {