diff --git a/src/torch/ops/flash_attn_varlen_func/flash_attn_varlen_func.cc b/src/torch/ops/flash_attn_varlen_func/flash_attn_varlen_func.cc
index ab3a350f5..9adc783fa 100644
--- a/src/torch/ops/flash_attn_varlen_func/flash_attn_varlen_func.cc
+++ b/src/torch/ops/flash_attn_varlen_func/flash_attn_varlen_func.cc
@@ -1,6 +1,7 @@
 #include "torch/ops/flash_attn_varlen_func/flash_attn_varlen_func.h"
 
 #include <ATen/ops/_flash_attention_forward.h>
+#include <ATen/ops/arange.h>
 #include <c10/cuda/CUDAGuard.h>
 #include <c10/cuda/CUDAStream.h>
 #include <cuda_runtime_api.h>
@@ -76,7 +77,26 @@ void Operator<FlashAttnVarlenFunc, Device::Type::kNvidia, 8>::operator()(
     // by copying them into caller-provided buffers on the selected CUDA stream.
     at_out.copy_(std::get<0>(result));
     if (at_softmax_lse.has_value()) {
-      at_softmax_lse->copy_(std::get<1>(result));
+      const auto& result_softmax_lse = std::get<1>(result);
+      if (result_softmax_lse.dim() == 3) {
+        // ATen may return padded (batch, heads, max_q) storage instead of the
+        // packed FlashAttention (heads, total_q) layout.
+        const auto batch_size = result_softmax_lse.size(0);
+        const auto q_lengths = at_cu_seqlens_q.narrow(0, 1, batch_size) -
+                               at_cu_seqlens_q.narrow(0, 0, batch_size);
+        const auto positions =
+            at::arange(result_softmax_lse.size(2), at_cu_seqlens_q.options());
+        const auto valid_positions =
+            positions.unsqueeze(0).lt(q_lengths.unsqueeze(1));
+        const auto packed_softmax_lse =
+            result_softmax_lse.transpose(1, 2)
+                .masked_select(valid_positions.unsqueeze(2))
+                .view({at_q.size(0), at_q.size(1)})
+                .transpose(0, 1);
+        at_softmax_lse->copy_(packed_softmax_lse);
+      } else {
+        at_softmax_lse->copy_(result_softmax_lse);
+      }
       at_s_dmask->copy_(std::get<4>(result));
     }
   };
diff --git a/tests/test_flash_attn_varlen_func.py b/tests/test_flash_attn_varlen_func.py
index 80e778e35..b17879deb 100644
--- a/tests/test_flash_attn_varlen_func.py
+++ b/tests/test_flash_attn_varlen_func.py
@@ -114,7 +114,11 @@ def test_flash_attn_varlen_func(
             0 if causal else None if window_size[1] < 0 else window_size[1]
         ),
     )
-    torch.testing.assert_close(softmax_lse, expected_auxiliary[1])
+    expected_softmax_lse = _pack_varlen_softmax_lse(
+        expected_auxiliary[1],
+        q_lens,
+    )
+    torch.testing.assert_close(softmax_lse, expected_softmax_lse)
     torch.testing.assert_close(s_dmask, expected_auxiliary[4])
 
 
@@ -298,6 +302,18 @@ def _cumulative_lengths(lengths, device):
     return torch.tensor(values, dtype=torch.int32, device=device)
 
 
+def _pack_varlen_softmax_lse(softmax_lse, q_lens):
+    if softmax_lse.ndim == 2:
+        return softmax_lse
+
+    return torch.cat(
+        tuple(
+            sequence_lse[:, :q_len] for sequence_lse, q_len in zip(softmax_lse, q_lens)
+        ),
+        dim=1,
+    )
+
+
 def _reference_varlen_attention(
     q,
     k,