diff --git a/js/web/lib/wasm/jsep/webgpu/ops/scatter-nd.ts b/js/web/lib/wasm/jsep/webgpu/ops/scatter-nd.ts
index 7fd0c2ef42aff..ec1d23e4887d5 100644
--- a/js/web/lib/wasm/jsep/webgpu/ops/scatter-nd.ts
+++ b/js/web/lib/wasm/jsep/webgpu/ops/scatter-nd.ts
@@ -78,6 +78,36 @@ const atomicReductionSnippet = (reduction: string, ptr: string, v: string, type:
   }
 };
 
+const calcDataOffsetSnippet = (dataRank: number, parallel: boolean) =>
+  `${
+    dataRank === 1
+      ? `
+    let element_count_dim = uniforms.output_strides;
+    let dim_value = uniforms.output_shape;`
+      : `
+    let element_count_dim = uniforms.output_strides[${parallel ? 'i - indices_start' : 'i'}];
+    let dim_value = uniforms.output_shape[${parallel ? 'i - indices_start' : 'i'} + uniforms.last_index_dimension];`
+  }
+    
+    if (index >= 0) {
+      if (index >= i32(dim_value)) {
+        index = i32(dim_value - 1);
+      }
+    } else {
+      if (index < -i32(dim_value)) {
+        index = 0;
+      } else {
+        index += i32(dim_value);
+      }
+    }
+    data_offset += u32((u32(index) * element_count_dim));`;
+
+const updateElementsSnippet = (attributes: ScatterNDAttributes, outputTypeValue: ReductionType, parallel: boolean) =>
+  `for (var i = 0u; i < uniforms.num_updates_elements; i++) {
+        let value = updates[uniforms.num_updates_elements * ${parallel ? 'global_idx' : 'idx'} + i];
+        ${atomicReductionSnippet(attributes.reduction, 'output[data_offset + i]', 'value', outputTypeValue)}
+      }`;
+
 const createScatterNDProgramInfo = (inputs: readonly TensorView[], attributes: ScatterNDAttributes): ProgramInfo => {
   const inputShape = inputs[0].dims;
   const indicesShape = inputs[1].dims;
@@ -87,6 +117,7 @@ const createScatterNDProgramInfo = (inputs: readonly TensorView[], attributes: S
   const outputSize = Math.ceil(ShapeUtil.size(indicesShape) / components);
   const lastIndexDimension = indicesShape[indicesShape.length - 1];
   const numUpdatesElements = ShapeUtil.sizeFromDimension(inputShape, lastIndexDimension);
+  const numIndicesElements = ShapeUtil.sizeFromDimension(indicesShape, 0) / lastIndexDimension;
 
   const programUniforms: ProgramUniform[] = [
     { type: DataType.uint32, data: outputSize },
@@ -113,9 +144,8 @@ const createScatterNDProgramInfo = (inputs: readonly TensorView[], attributes: S
         ${shaderHelper.guardAgainstOutOfBoundsWorkgroupSizes('uniforms.output_size')}
   var hasDuplicates = false;
   if (${attributes.reduction === 'none'}) {
-    let n = ${ShapeUtil.size(indicesShape)};
-    for (var i = 0; i < n; i = i + 1) {
-      for (var j = i + 1; j < n; j = j + 1) {
+    for (var i = 0; i < ${numIndicesElements}; i = i + 1) {
+      for (var j = i + 1; j < ${numIndicesElements}; j = j + 1) {
         var index_i = i32(indices[i].x);
         var index_j = i32(indices[j].x);
         if (index_i == index_j) {
@@ -129,51 +159,31 @@ const createScatterNDProgramInfo = (inputs: readonly TensorView[], attributes: S
     }
   }
 
-  var data_offset = 0u;
-  var indices_start = uniforms.last_index_dimension * global_idx;
   if (${attributes.reduction === 'none'} && hasDuplicates) {
     if (global_idx != 0u) {
       return;
     }
-    indices_start = 0u;
-  }
-  let indices_end = indices_start + uniforms.last_index_dimension;
-  for (var i = indices_start; i < indices_end; i++) {
-    var index = i32(indices[i].x);
-    ${
-      inputs[0].dims.length === 1
-        ? `
-    let element_count_dim = uniforms.output_strides;
-    let dim_value = uniforms.output_shape;`
-        : `
-    let element_count_dim = uniforms.output_strides[i - indices_start];
-    let dim_value = uniforms.output_shape[i - indices_start + uniforms.last_index_dimension];`
-    }
-    if (index >= 0) {
-      if (index >= i32(dim_value)) {
-        index = i32(dim_value - 1);
-      }
-    } else {
-      if (index < -i32(dim_value)) {
-        index = 0;
-      } else {
-        index += i32(dim_value);
+    // Process each index-update pair individually when duplicates exist
+    for (var idx = 0u; idx < ${numIndicesElements}u; idx++) {
+      var data_offset = 0u;
+      for (var i = 0u; i < uniforms.last_index_dimension; i++) {
+        var index = i32(indices[idx * uniforms.last_index_dimension + i].x);
+        ${calcDataOffsetSnippet(inputShape.length, false)}
       }
+      ${updateElementsSnippet(attributes, output.type.value as ReductionType, false)}
     }
-    data_offset += u32((u32(index) * element_count_dim));
+    return;
   }
 
-  for (var i = 0u; i < uniforms.num_updates_elements; i++) {
-    let value = updates[uniforms.num_updates_elements * global_idx + i];
-    ${atomicReductionSnippet(
-      attributes.reduction,
-      'output[data_offset + i]',
-      'value',
-      output.type.value as ReductionType,
-    )}
+  var data_offset = 0u;
+  var indices_start = uniforms.last_index_dimension * global_idx;
+  var indices_end = indices_start + uniforms.last_index_dimension;
+  for (var i = indices_start; i < indices_end; i++) {
+    var index = i32(indices[i].x);
+    ${calcDataOffsetSnippet(inputShape.length, true)}
   }
-
-      }`;
+  ${updateElementsSnippet(attributes, output.type.value as ReductionType, true)}
+  }`;
   };
   return {
     name: 'ScatterND',