diff --git a/python/sglang/srt/layers/radix_attention.py b/python/sglang/srt/layers/radix_attention.py
index c522c972585..355960367c0 100644
--- a/python/sglang/srt/layers/radix_attention.py
+++ b/python/sglang/srt/layers/radix_attention.py
@@ -85,9 +85,9 @@ def decode_forward_triton(self, q, k, v, input_metadata: InputMetadata):
         return o
 
     def extend_forward_flashinfer(self, q, k, v, input_metadata: InputMetadata):
-        self.store_kv_cache(k, v, input_metadata)
+        if not input_metadata.use_ragged:
+            self.store_kv_cache(k, v, input_metadata)
 
-        if input_metadata.total_num_tokens <= 4096:
             o = input_metadata.flashinfer_prefill_wrapper_paged.forward(
                 q.contiguous().view(-1, self.tp_q_head_num, self.head_dim),
                 input_metadata.token_to_kv_pool.get_kv_buffer(self.layer_id),
@@ -122,6 +122,8 @@ def extend_forward_flashinfer(self, q, k, v, input_metadata: InputMetadata):
 
                 o, _ = merge_state(o1, s1, o2, s2)
 
+            self.store_kv_cache(k, v, input_metadata)
+
             if input_metadata.total_num_tokens >= global_config.layer_sync_threshold:
                 torch.cuda.synchronize()
 
diff --git a/python/sglang/srt/managers/controller/infer_batch.py b/python/sglang/srt/managers/controller/infer_batch.py
index 58136d4b81c..e7c5ab5f713 100644
--- a/python/sglang/srt/managers/controller/infer_batch.py
+++ b/python/sglang/srt/managers/controller/infer_batch.py
@@ -726,6 +726,7 @@ class InputMetadata:
     flashinfer_prefill_wrapper_ragged: "BatchPrefillWithRaggedKVCacheWrapper" = None
     flashinfer_prefill_wrapper_paged: "BatchPrefillWithPagedKVCacheWrapper" = None
     flashinfer_decode_wrapper: "BatchDecodeWithPagedKVCacheWrapper" = None
+    use_ragged: bool = False
 
     @classmethod
     def create(
@@ -741,7 +742,10 @@ def create(
         return_logprob=False,
         skip_flashinfer_init=False,
     ):
+        use_ragged = False
         if not skip_flashinfer_init and not model_runner.server_args.disable_flashinfer:
+            if forward_mode != ForwardMode.DECODE and int(torch.sum(seq_lens)) > 4096:
+                use_ragged = True
             init_flashinfer_args(
                 forward_mode,
                 model_runner,
@@ -749,6 +753,7 @@ def create(
                 seq_lens,
                 prefix_lens,
                 model_runner.flashinfer_decode_wrapper,
+                use_ragged,
             )
 
         batch_size = len(req_pool_indices)
@@ -803,6 +808,7 @@ def create(
             flashinfer_prefill_wrapper_ragged=model_runner.flashinfer_prefill_wrapper_ragged,
             flashinfer_prefill_wrapper_paged=model_runner.flashinfer_prefill_wrapper_paged,
             flashinfer_decode_wrapper=model_runner.flashinfer_decode_wrapper,
+            use_ragged=use_ragged,
         )
 
         if model_runner.server_args.disable_flashinfer:
@@ -823,6 +829,7 @@ def init_flashinfer_args(
     seq_lens,
     prefix_lens,
     flashinfer_decode_wrapper,
+    use_ragged=False,
 ):
     """Init auxiliary variables for FlashInfer attention backend."""
     num_qo_heads = model_runner.model_config.num_attention_heads // model_runner.tp_size
@@ -831,10 +838,10 @@ def init_flashinfer_args(
     batch_size = len(req_pool_indices)
     total_num_tokens = int(torch.sum(seq_lens))
 
-    if forward_mode == ForwardMode.DECODE or total_num_tokens <= 4096:
-        paged_kernel_lens = seq_lens
-    else:
+    if use_ragged:
         paged_kernel_lens = prefix_lens
+    else:
+        paged_kernel_lens = seq_lens
 
     kv_indptr = torch.zeros((batch_size + 1,), dtype=torch.int32, device="cuda")
     kv_indptr[1:] = torch.cumsum(paged_kernel_lens, dim=0)
@@ -867,14 +874,15 @@ def init_flashinfer_args(
         qo_indptr = torch.zeros((batch_size + 1,), dtype=torch.int32, device="cuda")
         qo_indptr[1:] = torch.cumsum(seq_lens - prefix_lens, dim=0)
 
-        model_runner.flashinfer_prefill_wrapper_ragged.end_forward()
-        model_runner.flashinfer_prefill_wrapper_ragged.begin_forward(
-            qo_indptr,
-            qo_indptr,
-            num_qo_heads,
-            num_kv_heads,
-            head_dim,
-        )
+        if use_ragged:
+            model_runner.flashinfer_prefill_wrapper_ragged.end_forward()
+            model_runner.flashinfer_prefill_wrapper_ragged.begin_forward(
+                qo_indptr,
+                qo_indptr,
+                num_qo_heads,
+                num_kv_heads,
+                head_dim,
+            )
 
         # cached part
         model_runner.flashinfer_prefill_wrapper_paged.end_forward()