diff --git a/server/consumer.go b/server/consumer.go
index 552f7f457b..db1743cb17 100644
--- a/server/consumer.go
+++ b/server/consumer.go
@@ -5835,10 +5835,6 @@ func (o *consumer) requestNextMsgSubject() string {
 
 func (o *consumer) decStreamPending(sseq uint64, subj string) {
 	o.mu.Lock()
-	// Update our cached num pending only if we think deliverMsg has not done so.
-	if sseq >= o.sseq && o.isFilteredMatch(subj) {
-		o.npc--
-	}
 
 	// Check if this message was pending.
 	p, wasPending := o.pending[sseq]
@@ -5846,6 +5842,15 @@ func (o *consumer) decStreamPending(sseq uint64, subj string) {
 	if o.rdc != nil {
 		rdc = o.rdc[sseq]
 	}
+
+	// Update our cached num pending only if we think deliverMsg has not done so.
+	// Either we have not reached the message yet, or we've hit the race condition
+	// when there is contention at the beginning of the stream. In which case we can
+	// only decrement if the ack floor is still low enough to be able to detect it.
+	if o.isFilteredMatch(subj) && sseq > o.asflr && (sseq >= o.sseq || !wasPending) {
+		o.npc--
+	}
+
 	o.mu.Unlock()
 
 	// If it was pending process it like an ack.
diff --git a/server/jetstream_test.go b/server/jetstream_test.go
index d5d20ae89c..f578b12307 100644
--- a/server/jetstream_test.go
+++ b/server/jetstream_test.go
@@ -24737,3 +24737,68 @@ func TestJetStreamWouldExceedLimits(t *testing.T) {
 	require_True(t, js.wouldExceedLimits(MemoryStorage, int(js.config.MaxMemory)+1))
 	require_True(t, js.wouldExceedLimits(FileStorage, int(js.config.MaxStore)+1))
 }
+
+func TestJetStreamConsumerDecrementPendingCountOnSkippedMsg(t *testing.T) {
+	s := RunBasicJetStreamServer(t)
+	defer s.Shutdown()
+
+	nc, js := jsClientConnect(t, s)
+	defer nc.Close()
+
+	_, err := js.AddStream(&nats.StreamConfig{Name: "TEST", Subjects: []string{"foo"}})
+	require_NoError(t, err)
+
+	_, err = js.AddConsumer("TEST", &nats.ConsumerConfig{Durable: "CONSUMER"})
+	require_NoError(t, err)
+
+	acc, err := s.lookupAccount(globalAccountName)
+	require_NoError(t, err)
+	mset, err := acc.lookupStream("TEST")
+	require_NoError(t, err)
+	o := mset.lookupConsumer("CONSUMER")
+
+	requireExpected := func(expected int64) {
+		t.Helper()
+		o.mu.RLock()
+		defer o.mu.RUnlock()
+		require_Equal(t, o.npc, expected)
+	}
+
+	// Should initially report no messages available.
+	requireExpected(0)
+
+	// A new message is available, should report in pending.
+	_, err = js.Publish("foo", nil)
+	require_NoError(t, err)
+	requireExpected(1)
+
+	// Pending count should decrease when the message is deleted.
+	err = js.DeleteMsg("TEST", 1)
+	require_NoError(t, err)
+	requireExpected(0)
+
+	// Make more messages available, should report in pending.
+	_, err = js.Publish("foo", nil)
+	require_NoError(t, err)
+	_, err = js.Publish("foo", nil)
+	require_NoError(t, err)
+	requireExpected(2)
+
+	// Simulate getNextMsg being called and the starting sequence to skip over a deleted message.
+	// Also simulate one pending message.
+	o.mu.Lock()
+	o.sseq = 100
+	o.npc--
+	o.pending = make(map[uint64]*Pending)
+	o.pending[2] = &Pending{}
+	o.mu.Unlock()
+
+	// Since this message is pending we should not decrement pending count as we've done so already.
+	o.decStreamPending(2, "foo")
+	requireExpected(1)
+
+	// This is the deleted message that was skipped, and we can decrement the pending count
+	// because it's not pending and only as long as the ack floor hasn't moved up yet.
+	o.decStreamPending(3, "foo")
+	requireExpected(0)
+}