diff --git a/python/sglang/srt/managers/scheduler.py b/python/sglang/srt/managers/scheduler.py
index 1a18102fd..1e74d2f8e 100644
--- a/python/sglang/srt/managers/scheduler.py
+++ b/python/sglang/srt/managers/scheduler.py
@@ -2654,6 +2654,11 @@ class Scheduler(
         return ClearHiCacheReqOutput(success=if_success)
 
     def is_fully_idle(self, for_health_check=False) -> bool:
+        # Health check piggybacks on running requests in process_output.
+        # Only running_batch + waiting_queue guarantee active GPU processing;
+        # disagg queues (bootstrap/prealloc/transfer) may have items without
+        # any request actually running on GPU — e.g. stuck handshake, full
+        # KV cache, or stalled transfer — so they can't carry health info.
         # Batch running status
         idle = (
             self.running_batch.is_empty()
@@ -2667,13 +2672,6 @@ class Scheduler(
 
         # Waiting queues: waiting + bootstrapping + preallocation + kv transfer (decode)
         idle &= len(self.waiting_queue) == 0
-        if self.disaggregation_mode == DisaggregationMode.PREFILL:
-            idle &= len(self.disagg_prefill_bootstrap_queue.queue) == 0
-        if self.disaggregation_mode == DisaggregationMode.DECODE:
-            idle &= (
-                len(self.disagg_decode_prealloc_queue.queue) == 0
-                and len(self.disagg_decode_transfer_queue.queue) == 0
-            )
 
         if not for_health_check:
             # Grammar queue and prefill inflight queue may not produce batch results
@@ -2681,6 +2679,11 @@ class Scheduler(
             idle &= len(self.grammar_manager.grammar_queue) == 0
             if self.disaggregation_mode == DisaggregationMode.PREFILL:
                 idle &= len(self.disagg_prefill_inflight_queue) == 0
+                idle &= len(self.disagg_prefill_bootstrap_queue.queue) == 0
+
+            if self.disaggregation_mode == DisaggregationMode.DECODE:
+                idle &= len(self.disagg_decode_prealloc_queue.queue) == 0
+                idle &= len(self.disagg_decode_transfer_queue.queue) == 0
 
         return idle