diff --git a/vllm/v1/core/sched/scheduler.py b/vllm/v1/core/sched/scheduler.py
index 20a40d74f311..263eec777a84 100644
--- a/vllm/v1/core/sched/scheduler.py
+++ b/vllm/v1/core/sched/scheduler.py
@@ -580,6 +580,13 @@ def schedule(self) -> SchedulerOutput:
             batch = KVEventBatch(ts=time.time(), events=events)
             self.kv_event_publisher.publish(batch)
 
+        self._update_after_schedule(scheduler_output)
+        return scheduler_output
+
+    def _update_after_schedule(
+        self,
+        scheduler_output: SchedulerOutput,
+    ) -> None:
         # Advance the number of computed tokens for the request AFTER
         # the request is scheduled.
         # 1. The scheduler_output of the current step has to include the
@@ -589,11 +596,15 @@ def schedule(self) -> SchedulerOutput:
         #    scheduling step.
         # 3. If some tokens (e.g. spec tokens) are rejected later, the number of
         #    computed tokens will be adjusted in update_from_output.
+        num_scheduled_tokens = scheduler_output.num_scheduled_tokens
         for req_id, num_scheduled_token in num_scheduled_tokens.items():
-            self.requests[req_id].num_computed_tokens += num_scheduled_token
+            request = self.requests[req_id]
+            request.num_computed_tokens += num_scheduled_token
 
+        # Clear the finished request IDs.
+        # NOTE: We shouldn't do self.finished_req_ids.clear() here because
+        # it will also affect the scheduler output.
         self.finished_req_ids = set()
-        return scheduler_output
 
     def _make_cached_request_data(
         self,
@@ -763,19 +774,10 @@ def update_from_output(
                     num_draft_tokens=len(scheduled_spec_token_ids),
                     num_accepted_tokens=len(generated_token_ids) - 1)
 
-            cached_encoder_input_ids = (
-                self.encoder_cache_manager.get_cached_input_ids(request))
-            # OPTIMIZATION: Avoid list(set) if the set is empty.
-            if cached_encoder_input_ids:
-                for input_id in list(cached_encoder_input_ids):
-                    mm_positions = request.mm_positions[input_id]
-                    start_pos = mm_positions.offset
-                    num_tokens = mm_positions.length
-                    if start_pos + num_tokens <= request.num_computed_tokens:
-                        # The encoder output is already processed and stored
-                        # in the decoder's KV cache.
-                        self.encoder_cache_manager.free_encoder_input(
-                            request, input_id)
+            # NOTE(woosuk): This has to be executed after updating
+            # `request.num_computed_tokens`.
+            if request.has_encoder_inputs:
+                self._free_encoder_inputs(request)
 
             stopped = False
             new_logprobs = None
@@ -891,6 +893,25 @@ def update_from_output(
 
         return engine_core_outputs
 
+    def _free_encoder_inputs(self, request: Request) -> None:
+        cached_encoder_input_ids = (
+            self.encoder_cache_manager.get_cached_input_ids(request))
+        # OPTIMIZATION: Avoid list(set) if the set is empty.
+        if not cached_encoder_input_ids:
+            return
+
+        # Here, we use list(set) to avoid modifying the set while iterating
+        # over it.
+        for input_id in list(cached_encoder_input_ids):
+            mm_positions = request.mm_positions[input_id]
+            start_pos = mm_positions.offset
+            num_tokens = mm_positions.length
+            if start_pos + num_tokens <= request.num_computed_tokens:
+                # The encoder output is already processed and stored
+                # in the decoder's KV cache.
+                self.encoder_cache_manager.free_encoder_input(
+                    request, input_id)
+
     def get_request_counts(self) -> tuple[int, int]:
         """Returns (num_running_reqs, num_waiting_reqs)."""
         return len(self.running), len(self.waiting)