diff --git a/pkg/pattern/drain/drain.go b/pkg/pattern/drain/drain.go
index 784beabb2a876..d783e9d1919e3 100644
--- a/pkg/pattern/drain/drain.go
+++ b/pkg/pattern/drain/drain.go
@@ -284,6 +284,27 @@ func (d *Drain) PatternString(c *LogCluster) string {
 	return s
 }
 
+func (d *Drain) Prune() {
+	d.pruneTree(d.rootNode)
+}
+
+func (d *Drain) pruneTree(node *Node) int {
+	for key, child := range node.keyToChildNode {
+		if d.pruneTree(child) == 0 {
+			delete(node.keyToChildNode, key)
+		}
+	}
+
+	validClusterIds := 0
+	for _, clusterID := range node.clusterIDs {
+		cluster := d.idToCluster.Get(clusterID)
+		if cluster != nil {
+			validClusterIds++
+		}
+	}
+	return len(node.keyToChildNode) + validClusterIds
+}
+
 func (d *Drain) Delete(cluster *LogCluster) {
 	d.idToCluster.cache.Remove(cluster.id)
 }
diff --git a/pkg/pattern/drain/drain_test.go b/pkg/pattern/drain/drain_test.go
index 34bcf8b4c12a5..690db7da29ee8 100644
--- a/pkg/pattern/drain/drain_test.go
+++ b/pkg/pattern/drain/drain_test.go
@@ -6,6 +6,7 @@ import (
 	"os"
 	"strings"
 	"testing"
+	"time"
 
 	"github.com/stretchr/testify/require"
 	"golang.org/x/exp/slices"
@@ -625,3 +626,68 @@ func TestDeduplicatePlaceholders(b *testing.T) {
 		})
 	}
 }
+
+func TestDrain_PruneTreeClearsOldBranches(t *testing.T) {
+	t.Parallel()
+	tests := []struct {
+		name       string
+		drain      *Drain
+		inputLines []string
+	}{
+		{
+			name:  "should prune old branches",
+			drain: New(DefaultConfig(), nil),
+			inputLines: []string{
+				"test test test A",
+				"test test test B",
+				"test test test C",
+				"test test test D",
+				"test test test E",
+				"test test test F",
+				"test test test G",
+				"my name is W",
+				"my name is X",
+				"my name is Y",
+				"my name is Z",
+			},
+		},
+	}
+	for _, tt := range tests {
+		tt := tt
+		t.Run(tt.name, func(t *testing.T) {
+			now := time.Now()
+			for i, line := range tt.inputLines {
+				ts := now.Add(time.Millisecond * time.Duration(i))
+				if i < 7 {
+					ts = ts.Add(-time.Duration(7-i) * time.Minute)
+				}
+				tt.drain.Train(line, ts.UnixNano())
+			}
+
+			require.Len(t, tt.drain.Clusters(), 2)
+			require.Equal(t, 8, countNodes(tt.drain.rootNode))
+
+			clusters := tt.drain.Clusters()
+			for _, cluster := range clusters {
+				cluster.Prune(time.Second * 10)
+				if cluster.Size == 0 {
+					tt.drain.Delete(cluster)
+				}
+			}
+			require.Len(t, tt.drain.Clusters(), 1)
+			require.Equal(t, 8, countNodes(tt.drain.rootNode), "expected same number of nodes before pruning")
+
+			tt.drain.Prune()
+			require.Len(t, tt.drain.Clusters(), 1)
+			require.Equal(t, 5, countNodes(tt.drain.rootNode), "expected fewer nodes after pruning")
+		})
+	}
+}
+
+func countNodes(node *Node) int {
+	total := 1
+	for _, child := range node.keyToChildNode {
+		total += countNodes(child)
+	}
+	return total
+}
diff --git a/pkg/pattern/stream.go b/pkg/pattern/stream.go
index ec075fece7396..fef357eb1b40f 100644
--- a/pkg/pattern/stream.go
+++ b/pkg/pattern/stream.go
@@ -275,6 +275,8 @@ func (s *stream) prune(olderThan time.Duration) bool {
 			s.patterns.Delete(cluster)
 		}
 	}
+	// Clear empty branches after deleting chunks & clusters
+	s.patterns.Prune()
 
 	chunksPruned := true
 	if s.chunks != nil {