diff --git a/pkg/scheduler/backend/queue/scheduling_queue.go b/pkg/scheduler/backend/queue/scheduling_queue.go
index 826a5a0e09f..b1cf9d1e1bd 100644
--- a/pkg/scheduler/backend/queue/scheduling_queue.go
+++ b/pkg/scheduler/backend/queue/scheduling_queue.go
@@ -894,6 +894,8 @@ func (p *PriorityQueue) AddUnschedulableIfNotPresent(logger klog.Logger, pInfo *
 	// We changed ConsecutiveErrorsCount or UnschedulableCount plus Timestamp, and now the calculated backoff time should be different,
 	// removing the cached backoff time.
 	pInfo.BackoffExpiration = time.Time{}
+	// Clear the flush flag since the pod is returning to the queue after a scheduling attempt.
+	pInfo.WasFlushedFromUnschedulable = false
 
 	if !p.isSchedulingQueueHintEnabled {
 		// fall back to the old behavior which doesn't depend on the queueing hint.
@@ -949,7 +951,7 @@ func (p *PriorityQueue) flushUnschedulablePodsLeftover(logger klog.Logger) {
 		lastScheduleTime := pInfo.Timestamp
 		if currentTime.Sub(lastScheduleTime) > p.podMaxInUnschedulablePodsDuration {
 			// Mark this pod as flushed so we can detect if it schedules soon after
-			pInfo.FlushedFromUnschedulableAt = &currentTime
+			pInfo.WasFlushedFromUnschedulable = true
 			podsToMove = append(podsToMove, pInfo)
 		}
 	}
@@ -1237,6 +1239,13 @@ func (p *PriorityQueue) movePodsToActiveOrBackoffQueue(logger klog.Logger, podIn
 			continue
 		}
 
+		// Clear the flush flag if this pod is being moved by an event (not by timeout flush).
+		// EventUnschedulableTimeout is the event used by flushUnschedulablePodsLeftover,
+		// where the flag is set to true before calling this function.
+		if event != framework.EventUnschedulableTimeout {
+			pInfo.WasFlushedFromUnschedulable = false
+		}
+
 		p.unschedulablePods.delete(pInfo.Pod, pInfo.Gated())
 		queue := p.requeuePodWithQueueingStrategy(logger, pInfo, schedulingHint, event.Label())
 		if queue == activeQ || (p.isPopFromBackoffQEnabled && queue == backoffQ) {
diff --git a/pkg/scheduler/framework/types.go b/pkg/scheduler/framework/types.go
index de20feed86f..607f18ad683 100644
--- a/pkg/scheduler/framework/types.go
+++ b/pkg/scheduler/framework/types.go
@@ -526,10 +526,12 @@ type QueuedPodInfo struct {
 	// That's why we need to distinguish ConsecutiveErrorsCount for the error status and UnschedulableCount for the unschedulable status.
 	// See https://github.com/kubernetes/kubernetes/issues/128744 for the discussion.
 	ConsecutiveErrorsCount int
-	// FlushedFromUnschedulableAt tracks when this pod was last flushed from unschedulablePods
-	// due to timeout. This is used to detect if the pod becomes schedulable soon after flush,
-	// which may indicate missing queue hint optimizations or event handling bugs.
-	FlushedFromUnschedulableAt *time.Time
+	// WasFlushedFromUnschedulable tracks whether this pod was most recently moved to activeQ
+	// by the periodic flush from unschedulablePods due to timeout (rather than by an event).
+	// This is used to detect if the pod becomes schedulable soon after flush, which may
+	// indicate missing queue hint optimizations or event handling bugs.
+	// This flag is cleared when the pod returns to the queue for any reason.
+	WasFlushedFromUnschedulable bool
 	// The time when the pod is added to the queue for the first time. The pod may be added
 	// back to the queue multiple times before it's successfully scheduled.
 	// It shouldn't be updated once initialized. It's used to record the e2e scheduling
diff --git a/pkg/scheduler/schedule_one.go b/pkg/scheduler/schedule_one.go
index 4cc5ad717c4..4285ffe808d 100644
--- a/pkg/scheduler/schedule_one.go
+++ b/pkg/scheduler/schedule_one.go
@@ -341,7 +341,7 @@ func (sched *Scheduler) bindingCycle(
 		metrics.PodSchedulingSLIDuration.WithLabelValues(getAttemptsLabel(assumedPodInfo)).Observe(metrics.SinceInSeconds(*assumedPodInfo.InitialAttemptTimestamp))
 	}
 	// Count pods scheduled after being flushed from unschedulablePods
-	if assumedPodInfo.FlushedFromUnschedulableAt != nil {
+	if assumedPodInfo.WasFlushedFromUnschedulable {
 		metrics.PodScheduledAfterFlush.Inc()
 	}
 	// Run "postbind" plugins.