diff --git a/python/sglang/srt/speculative/eagle_utils.py b/python/sglang/srt/speculative/eagle_utils.py
index aa49e4fc7..d4741144d 100644
--- a/python/sglang/srt/speculative/eagle_utils.py
+++ b/python/sglang/srt/speculative/eagle_utils.py
@@ -177,11 +177,24 @@ class EagleDraftInput:
         )
         return kv_indices, cum_kv_seq_len, qo_indptr, None
 
-    def filter_batch(self, new_indices: torch.Tensor):
-        self.topk_p = self.topk_p[: len(new_indices)]
-        self.topk_index = self.topk_index[: len(new_indices)]
-        self.hidden_states = self.hidden_states[: len(new_indices)]
-        self.verified_id = self.verified_id[: len(new_indices)]
+    def filter_batch(self, new_indices: torch.Tensor, has_been_filtered: bool = True):
+        if has_been_filtered:
+            # in eagle_utils.py:verify, we have already filtered the batch by `unfinished_index`
+            # therefore, we don't need to filter the batch again in scheduler
+            if len(new_indices) != len(self.topk_p):
+                logger.warning(
+                    f"length of new_indices: {len(new_indices)} != length of topk_p: {len(self.topk_p)}, this should not happen"
+                )
+            self.topk_p = self.topk_p[: len(new_indices)]
+            self.topk_index = self.topk_index[: len(new_indices)]
+            self.hidden_states = self.hidden_states[: len(new_indices)]
+            self.verified_id = self.verified_id[: len(new_indices)]
+        else:
+            # in some cases(e.g draft_extend), we have not filtered the batch by `unfinished_index`
+            self.topk_p = self.topk_p[new_indices]
+            self.topk_index = self.topk_index[new_indices]
+            self.hidden_states = self.hidden_states[new_indices]
+            self.verified_id = self.verified_id[new_indices]
 
     def merge_batch(self, spec_info: EagleDraftInput):
         if self.hidden_states is None:
diff --git a/python/sglang/srt/speculative/eagle_worker.py b/python/sglang/srt/speculative/eagle_worker.py
index 8da0549e9..972d7182d 100644
--- a/python/sglang/srt/speculative/eagle_worker.py
+++ b/python/sglang/srt/speculative/eagle_worker.py
@@ -836,6 +836,21 @@ class EAGLEWorker(TpModelWorker):
         assert isinstance(forward_batch.spec_info, EagleDraftInput)
         assert forward_batch.spec_info is batch.spec_info
         self.capture_for_decode(logits_output, forward_batch.spec_info)
+        has_finished, unfinished_req_index = False, []
+        for i, req in enumerate(batch.reqs):
+            if req.finished():
+                has_finished = True
+            else:
+                unfinished_req_index.append(i)
+        if has_finished:
+            unfinished_index_device = torch.tensor(
+                unfinished_req_index,
+                dtype=torch.int64,
+                device=batch.spec_info.topk_p.device,
+            )
+            batch.spec_info.filter_batch(
+                unfinished_index_device, has_been_filtered=False
+            )
 
     def forward_draft_extend_after_decode(self, batch: ScheduleBatch):
         assert isinstance(batch.spec_info, EagleDraftInput)