diff --git a/js/web/test/data/ops/group-query-attention.jsonc b/js/web/test/data/ops/group-query-attention.jsonc
index 83a5dc765280e..b095b8e227d09 100644
--- a/js/web/test/data/ops/group-query-attention.jsonc
+++ b/js/web/test/data/ops/group-query-attention.jsonc
@@ -42,7 +42,7 @@
           },
           // seqlens_k
           {
-            "data": [1],
+            "data": [0],
             "dims": [1],
             "type": "int32"
           },
@@ -197,7 +197,7 @@
           },
           // seqlens_k
           {
-            "data": [3],
+            "data": [2],
             "dims": [1],
             "type": "int32"
           },
@@ -276,7 +276,7 @@
           },
           // seqlens_k
           {
-            "data": [3],
+            "data": [2],
             "dims": [1],
             "type": "int32"
           },
@@ -363,7 +363,7 @@
           },
           // seqlens_k
           {
-            "data": [3],
+            "data": [2],
             "dims": [1],
             "type": "int32"
           },
@@ -450,7 +450,7 @@
           },
           // seqlens_k
           {
-            "data": [1],
+            "data": [0],
             "dims": [1],
             "type": "int32"
           },
@@ -526,7 +526,7 @@
           },
           // seqlens_k
           {
-            "data": [3],
+            "data": [2],
             "dims": [1],
             "type": "int32"
           },
@@ -690,7 +690,7 @@
           },
           // seqlens_k
           {
-            "data": [1],
+            "data": [0],
             "dims": [1],
             "type": "int32"
           },
@@ -769,7 +769,7 @@
           },
           // seqlens_k
           {
-            "data": [1],
+            "data": [0],
             "dims": [1],
             "type": "int32"
           },
@@ -845,7 +845,7 @@
           },
           // seqlens_k
           {
-            "data": [1],
+            "data": [0],
             "dims": [1],
             "type": "int32"
           },
@@ -921,7 +921,7 @@
           },
           // seqlens_k
           {
-            "data": [2],
+            "data": [1],
             "dims": [1],
             "type": "int32"
           },
@@ -1006,7 +1006,7 @@
           },
           // seqlens_k
           {
-            "data": [1],
+            "data": [0],
             "dims": [1],
             "type": "int32"
           },
@@ -1100,7 +1100,7 @@
           },
           // seqlens_k
           {
-            "data": [4],
+            "data": [3],
             "dims": [1],
             "type": "int32"
           },
@@ -1186,7 +1186,7 @@
           },
           // seqlens_k
           {
-            "data": [1],
+            "data": [0],
             "dims": [1],
             "type": "int32"
           },
@@ -1269,7 +1269,7 @@
   //         },
   //         // seqlens_k
   //         {
-  //           "data": [3],
+  //           "data": [2],
   //           "dims": [1],
   //           "type": "int32"
   //         },
@@ -1363,7 +1363,7 @@
           },
           // seqlens_k
           {
-            "data": [3],
+            "data": [2],
             "dims": [1],
             "type": "int32"
           },
@@ -1455,7 +1455,7 @@
           },
           // seqlens_k -- legacy [1, 1] shape instead of [1]
           {
-            "data": [1],
+            "data": [0],
             "dims": [1, 1],
             "type": "int32"
           },
diff --git a/onnxruntime/contrib_ops/webgpu/bert/flash_attention_decode_qkv.wgsl.template b/onnxruntime/contrib_ops/webgpu/bert/flash_attention_decode_qkv.wgsl.template
index d5d2b89fcf29c..21029a25aa027 100644
--- a/onnxruntime/contrib_ops/webgpu/bert/flash_attention_decode_qkv.wgsl.template
+++ b/onnxruntime/contrib_ops/webgpu/bert/flash_attention_decode_qkv.wgsl.template
@@ -298,7 +298,7 @@ $MAIN {
     }
     workgroupBarrier();
 
-    if (local_idx < tile_size_k_vec) {
+    if (local_idx < tile_size_k_vec && k + local_idx < v_head_size_vec) {
       for (var m = 0u; m < m_tile && q_base + m < uniforms.new_sequence_length; m++) {
         for (var i = 0u; i < sub_tile_count; i++) {
           tile_output[m][k + local_idx] += qkv_values[m][i][local_idx];
@@ -326,7 +326,7 @@ $MAIN {
     }
     workgroupBarrier();
 
-    if (local_idx < tile_size_k_vec) {
+    if (local_idx < tile_size_k_vec && k + local_idx < v_head_size_vec) {
       for (var m = 0u; m < m_tile && q_base + m < uniforms.new_sequence_length; m++) {
         for (var i = 0u; i < sub_tile_count; i++) {
           tile_output[m][k + local_idx] += qkv_values[m][i][local_idx];