diff --git a/transformer_engine/pytorch/cpp_extensions/fused_attn.py b/transformer_engine/pytorch/cpp_extensions/fused_attn.py
index 7653296c78..06bfb6ef3c 100644
--- a/transformer_engine/pytorch/cpp_extensions/fused_attn.py
+++ b/transformer_engine/pytorch/cpp_extensions/fused_attn.py
@@ -363,13 +363,38 @@ def fused_attn_fwd(
         max_tensor = output_tensors[2]
         amax_dims = (0, 2) if max_tensor.ndim == 3 else (0, 2, 3)
 
-        if qkv_format == "thd" and max_tensor.ndim == 4:
-            # For THD on older cuDNN runtimes or THD on sm120, stats can be [b, h, sq, 1] with padded
-            # sequence positions. Exclude those padded positions when computing max_logit.
-            seqlens_q = (cu_seqlens_q[1:] - cu_seqlens_q[:-1]).to(device=max_tensor.device)
-            sq_idx = torch.arange(max_tensor.shape[2], device=max_tensor.device).view(1, 1, -1, 1)
-            valid = sq_idx < seqlens_q.view(-1, 1, 1, 1)
-            max_tensor = max_tensor.masked_fill(~valid, float("-inf"))
+        if qkv_format == "thd":
+            if max_tensor.ndim == 4:
+                # For THD on cuDNN <= 9.6 or THD on sm120, Max tensor can be [b, h, sq, 1]
+                # with padded sequence positions. Exclude those padded positions when computing max_logit.
+                seqlens_q = (cu_seqlens_q[1:] - cu_seqlens_q[:-1]).to(device=max_tensor.device)
+                sq_idx = torch.arange(max_tensor.shape[2], device=max_tensor.device).view(
+                    1, 1, -1, 1
+                )
+                valid = sq_idx < seqlens_q.view(-1, 1, 1, 1)
+                max_tensor = max_tensor.masked_fill(~valid, float("-inf"))
+            elif max_tensor.ndim == 3:
+                if cu_seqlens_q_padded is not None:
+                    # For THD + pad_between_seqs=True + non-sm120 + cuDNN>9.6, Max tensor is [tq, h, 1]
+                    # and padding positions could be uninitialized. Exclude those padded positions when
+                    # computing max_logit.
+                    actual_seqlens = (cu_seqlens_q[1:] - cu_seqlens_q[:-1]).to(
+                        device=max_tensor.device
+                    )
+                    padded_seqlens = (cu_seqlens_q_padded[1:] - cu_seqlens_q_padded[:-1]).to(
+                        device=max_tensor.device
+                    )
+                    pad_lens = (padded_seqlens - actual_seqlens).to(device=max_tensor.device)
+                    b = pad_lens.shape[0]
+
+                    # Stack [actual, pad] per batch into counts: e.g. [3,1, 3,1, 2,2, 7,1]
+                    counts = torch.stack([actual_seqlens, pad_lens], dim=1).flatten()
+                    # Tile [T, F] per sequence: [T,F, T,F, T,F, T,F]
+                    values = torch.tensor([True, False], device=max_tensor.device).repeat(b)
+                    # Expand: T×3, F×1, T×3, F×1, T×2, F×2, T×7, F×1 → TTTF|TTTF|TTFF|TTTTTTTF
+                    valid = torch.repeat_interleave(values, counts)
+                    # Finally, replace invalid (F) positions with -inf
+                    max_tensor = max_tensor.masked_fill(~valid.view(-1, 1, 1), float("-inf"))
 
         # Max -> max_logit [h]
         max_logit = torch.amax(max_tensor, dim=amax_dims).to(dtype=output_tensors[0].dtype)