diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index 06d5540380..e4f15f5cb8 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -692,6 +692,7 @@ func main() {
 	}
 	if cfgFile.StorageConfig.TSDBConfig != nil {
 		cfg.tsdb.OutOfOrderTimeWindow = cfgFile.StorageConfig.TSDBConfig.OutOfOrderTimeWindow
+		cfg.tsdb.StaleSeriesCompactionThreshold = cfgFile.StorageConfig.TSDBConfig.StaleSeriesCompactionThreshold
 		if cfgFile.StorageConfig.TSDBConfig.Retention != nil {
 			if cfgFile.StorageConfig.TSDBConfig.Retention.Time > 0 {
 				cfg.tsdb.RetentionDuration = cfgFile.StorageConfig.TSDBConfig.Retention.Time
@@ -1943,6 +1944,7 @@ type tsdbOptions struct {
 	UseUncachedIO                  bool
 	BlockCompactionExcludeFunc     tsdb.BlockExcludeFilterFunc
 	BlockReloadInterval            model.Duration
+	StaleSeriesCompactionThreshold float64
 }
 
 func (opts tsdbOptions) ToTSDBOptions() tsdb.Options {
@@ -1969,6 +1971,7 @@ func (opts tsdbOptions) ToTSDBOptions() tsdb.Options {
 		BlockCompactionExcludeFunc:     opts.BlockCompactionExcludeFunc,
 		BlockReloadInterval:            time.Duration(opts.BlockReloadInterval),
 		FeatureRegistry:                features.DefaultRegistry,
+		StaleSeriesCompactionThreshold: opts.StaleSeriesCompactionThreshold,
 	}
 }
 
diff --git a/config/config.go b/config/config.go
index 0b9b059ab2..d721d7fb86 100644
--- a/config/config.go
+++ b/config/config.go
@@ -1107,6 +1107,10 @@ type TSDBConfig struct {
 	// This should not be used directly and must be converted into OutOfOrderTimeWindow.
 	OutOfOrderTimeWindowFlag model.Duration `yaml:"out_of_order_time_window,omitempty"`
 
+	// StaleSeriesCompactionThreshold is a number between 0.0-1.0 indicating the % of stale series in
+	// the in-memory Head block. If the % of stale series crosses this threshold, stale series compaction is run immediately.
+	StaleSeriesCompactionThreshold float64 `yaml:"stale_series_compaction_threshold,omitempty"`
+
 	Retention *TSDBRetentionConfig `yaml:"retention,omitempty"`
 }
 
diff --git a/tsdb/db.go b/tsdb/db.go
index e3b00a2d11..1dd524a76a 100644
--- a/tsdb/db.go
+++ b/tsdb/db.go
@@ -100,6 +100,10 @@ func DefaultOptions() *Options {
 
 // Options of the DB storage.
 type Options struct {
+	// staleSeriesCompactionThreshold is same as below option with same name, but is atomic so that we can do live updates without locks.
+	// This is the one that must be used by the code.
+	staleSeriesCompactionThreshold atomic.Float64
+
 	// Segments (wal files) max size.
 	// WALSegmentSize = 0, segment size is default size.
 	// WALSegmentSize > 0, segment size is WALSegmentSize.
@@ -245,6 +249,10 @@ type Options struct {
 
 	// FeatureRegistry is used to register TSDB features.
 	FeatureRegistry features.Collector
+
+	// StaleSeriesCompactionThreshold is a number between 0.0-1.0 indicating the % of stale series in
+	// the in-memory Head block. If the % of stale series crosses this threshold, stale series compaction is run immediately.
+	StaleSeriesCompactionThreshold float64
 }
 
 type NewCompactorFunc func(ctx context.Context, r prometheus.Registerer, l *slog.Logger, ranges []int64, pool chunkenc.Pool, opts *Options) (Compactor, error)
@@ -305,6 +313,10 @@ type DB struct {
 	// out-of-order compaction and vertical queries.
 	oooWasEnabled atomic.Bool
 
+	// lastHeadCompactionTime is the last wall clock time when the head block compaction was started,
+	// irrespective of success or failure. This does not include out-of-order compaction and stale series compaction.
+	lastHeadCompactionTime time.Time
+
 	writeNotified wlog.WriteNotified
 
 	registerer prometheus.Registerer
@@ -857,6 +869,8 @@ func validateOpts(opts *Options, rngs []int64) (*Options, []int64) {
 		// configured maximum block duration.
 		rngs = ExponentialBlockRanges(opts.MinBlockDuration, 10, 3)
 	}
+
+	opts.staleSeriesCompactionThreshold.Store(opts.StaleSeriesCompactionThreshold)
 	return opts, rngs
 }
 
@@ -1151,6 +1165,28 @@ func (db *DB) run(ctx context.Context) {
 			}
 			// We attempt mmapping of head chunks regularly.
 			db.head.mmapHeadChunks()
+
+			numStaleSeries, numSeries := db.Head().NumStaleSeries(), db.Head().NumSeries()
+			staleSeriesRatio := float64(numStaleSeries) / float64(numSeries)
+			if db.autoCompact && db.opts.staleSeriesCompactionThreshold.Load() > 0 &&
+				staleSeriesRatio >= db.opts.staleSeriesCompactionThreshold.Load() {
+				nextCompactionIsSoon := false
+				if !db.lastHeadCompactionTime.IsZero() {
+					compactionInterval := time.Duration(db.head.chunkRange.Load()) * time.Millisecond
+					nextEstimatedCompactionTime := db.lastHeadCompactionTime.Add(compactionInterval)
+					if time.Now().Add(10 * time.Minute).After(nextEstimatedCompactionTime) {
+						// Next compaction is starting within next 10 mins.
+						nextCompactionIsSoon = true
+					}
+				}
+
+				if !nextCompactionIsSoon {
+					if err := db.CompactStaleHead(); err != nil {
+						db.logger.Error("immediate stale series compaction failed", "err", err)
+					}
+				}
+			}
+
 		case <-db.compactc:
 			db.metrics.compactionsTriggered.Inc()
 
@@ -1203,7 +1239,7 @@ func (db *DB) ApplyConfig(conf *config.Config) error {
 	oooTimeWindow := int64(0)
 	if conf.StorageConfig.TSDBConfig != nil {
 		oooTimeWindow = conf.StorageConfig.TSDBConfig.OutOfOrderTimeWindow
-
+		db.opts.staleSeriesCompactionThreshold.Store(conf.StorageConfig.TSDBConfig.StaleSeriesCompactionThreshold)
 		// Update retention configuration if provided.
 		if conf.StorageConfig.TSDBConfig.Retention != nil {
 			db.retentionMtx.Lock()
@@ -1217,6 +1253,8 @@ func (db *DB) ApplyConfig(conf *config.Config) error {
 			}
 			db.retentionMtx.Unlock()
 		}
+	} else {
+		db.opts.staleSeriesCompactionThreshold.Store(0)
 	}
 	if oooTimeWindow < 0 {
 		oooTimeWindow = 0
@@ -1560,6 +1598,8 @@ func (db *DB) compactOOO(dest string, oooHead *OOOCompactionHead) (_ []ulid.ULID
 // compactHead compacts the given RangeHead.
 // The db.cmtx should be held before calling this method.
 func (db *DB) compactHead(head *RangeHead) error {
+	db.lastHeadCompactionTime = time.Now()
+
 	uids, err := db.compactor.Write(db.dir, head, head.MinTime(), head.BlockMaxTime(), nil)
 	if err != nil {
 		return fmt.Errorf("persist head block: %w", err)