diff --git a/onnxruntime/core/optimizer/layout_transformation/layout_transformation.cc b/onnxruntime/core/optimizer/layout_transformation/layout_transformation.cc
index 4505d4afdf1e0..109ce66a6062a 100644
--- a/onnxruntime/core/optimizer/layout_transformation/layout_transformation.cc
+++ b/onnxruntime/core/optimizer/layout_transformation/layout_transformation.cc
@@ -162,7 +162,8 @@ Status TransformLayoutForEP(Graph& graph, bool& modified, const IExecutionProvid
       // Except for resize and convolution ops, all the other layout sensitive ops only require layout transformation
       // for 0th input and output. For resize, add the other relevant inputs which need conversion. For Conv - layout
       // transformer only converts layout for 0th input, weights should be handled by every EP.
-      if (node->OpType() == "Resize") {
+      // For resize in WebNN EP, we don't want to convert all the inputs except the 0th input.
+      if (node->OpType() == "Resize" && node->GetExecutionProviderType() != kWebNNExecutionProvider) {
         // Older versions of resize have a bug where ROI and Scales cannot be made empty inputs. To handle this case,
         // we need to jump a few extra hoops to make sure its inputs are correctly handled.
         //
diff --git a/onnxruntime/core/providers/webnn/builders/impl/resize_op_builder.cc b/onnxruntime/core/providers/webnn/builders/impl/resize_op_builder.cc
index 2afef28b10d0b..33f6b3f274105 100644
--- a/onnxruntime/core/providers/webnn/builders/impl/resize_op_builder.cc
+++ b/onnxruntime/core/providers/webnn/builders/impl/resize_op_builder.cc
@@ -123,11 +123,7 @@ Status ResizeOpBuilder::AddToModelBuilderImpl(ModelBuilder& model_builder,
   const bool isNhwc = model_builder.GetPreferredLayout() == DataLayout::NHWC;
   if (input_defs.size() == 3) {  // Use scales.
     ORT_RETURN_IF_NOT(GetResizeScales(initializers, node, scales, logger), "Error getting resize scales");
-    if (isNhwc) {
-      scales_hw = {scales[1], scales[2]};
-    } else {
-      scales_hw = {scales[2], scales[3]};
-    }
+    scales_hw = {scales[2], scales[3]};
     options.set("scales", emscripten::val::array(scales_hw));
   } else {  // We already checked number of inputs in IsOpSupportedImpl.
     std::vector<int64_t> output_sizes;
@@ -136,11 +132,7 @@ Status ResizeOpBuilder::AddToModelBuilderImpl(ModelBuilder& model_builder,
     std::transform(output_sizes.cbegin(), output_sizes.cend(),
                    std::back_inserter(sizes),
                    [](int64_t dim) -> int32_t { return SafeInt<int32_t>(dim); });
-    if (isNhwc) {
-      sizes_hw = {sizes[1], sizes[2]};
-    } else {
-      sizes_hw = {sizes[2], sizes[3]};
-    }
+    sizes_hw = {sizes[2], sizes[3]};
     options.set("sizes", emscripten::val::array(sizes_hw));
   }