diff --git a/onnxruntime/core/providers/webnn/builders/helper.cc b/onnxruntime/core/providers/webnn/builders/helper.cc
index 537e552af2763..f36f8283e9bf6 100644
--- a/onnxruntime/core/providers/webnn/builders/helper.cc
+++ b/onnxruntime/core/providers/webnn/builders/helper.cc
@@ -69,7 +69,8 @@ bool IsNodeSupported(const Node& node, const GraphViewer& graph_viewer, const We
   }
 }
 
-bool IsTensorShapeSupported(const NodeArg& node_arg, const std::string& parent_name, const logging::Logger& logger) {
+bool IsTensorShapeSupported(const NodeArg& node_arg, const std::string& parent_name,
+                            const logging::Logger& logger, bool allow_empty_input) {
   const auto& node_arg_name = node_arg.Name();
   const auto* shape_proto = node_arg.Shape();
   // Optional tensors can be indicated by an empty name, just ignore it.
@@ -89,7 +90,7 @@ bool IsTensorShapeSupported(const NodeArg& node_arg, const std::string& parent_n
                             << "use sessionOptions.FreeDimensionOverrides to set a fixed shape: " << node_arg_name;
       return false;
     }
-    if (dim.dim_value() == 0) {
+    if (dim.dim_value() == 0 && !allow_empty_input) {
       LOGS(logger, VERBOSE) << "The shape of [" << node_arg_name << "] has 0 dimension which is not supported by WebNN";
       return false;
     }
diff --git a/onnxruntime/core/providers/webnn/builders/helper.h b/onnxruntime/core/providers/webnn/builders/helper.h
index 23489f142df3e..7fdfc5aefa798 100644
--- a/onnxruntime/core/providers/webnn/builders/helper.h
+++ b/onnxruntime/core/providers/webnn/builders/helper.h
@@ -181,7 +181,8 @@ inline bool IsEmptyTensor(const InitializedTensorSet& initializers, const std::s
   return std::any_of(dims.begin(), dims.end(), [](auto d) { return d == 0; });
 }
 
-bool IsTensorShapeSupported(const NodeArg& node_arg, const std::string& parent_name, const logging::Logger& logger);
+bool IsTensorShapeSupported(const NodeArg& node_arg, const std::string& parent_name,
+                            const logging::Logger& logger, bool allow_empty_input = false);
 
 // Get a list of groups of supported nodes, each group represents a subgraph supported by WebNN EP.
 std::vector<std::vector<NodeIndex>> GetSupportedNodes(const GraphViewer& graph_viewer,
diff --git a/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.cc b/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.cc
index 704896e43a7e1..70fa0f9516c5c 100644
--- a/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.cc
+++ b/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.cc
@@ -45,7 +45,7 @@ bool BaseOpBuilder::HasSupportedInputs(const Node& node, const emscripten::val&
                                        const logging::Logger& logger) const {
   const auto node_name = MakeString("Node [", node.Name(), "] type [", node.OpType(), "]");
   for (const auto* input : node.InputDefs()) {
-    if (!IsTensorShapeSupported(*input, node_name, logger)) {
+    if (!IsTensorShapeSupported(*input, node_name, logger, allow_empty_tensor_as_input_)) {
       return false;
     }
   }
diff --git a/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.h b/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.h
index a632876dab2b9..9412fa8026fb3 100644
--- a/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.h
+++ b/onnxruntime/core/providers/webnn/builders/impl/base_op_builder.h
@@ -22,6 +22,9 @@ class BaseOpBuilder : public IOpBuilder {
                            const logging::Logger& logger) const override final ORT_MUST_USE_RESULT;
 
  protected:
+  explicit BaseOpBuilder(bool allow_empty_tensor_as_input = false)
+      : allow_empty_tensor_as_input_(allow_empty_tensor_as_input) {
+  }
   virtual Status AddToModelBuilderImpl(ModelBuilder& model_builder, const Node& node,
                                        const logging::Logger& logger) const ORT_MUST_USE_RESULT = 0;
 
@@ -55,6 +58,8 @@ class BaseOpBuilder : public IOpBuilder {
   bool HasSupportedOpSet(const Node& node, const logging::Logger& logger) const;
   bool HasSupportedInputs(const Node& node, const emscripten::val& wnn_limits, const logging::Logger& logger) const;
   bool HasSupportedOutputs(const Node& node, const emscripten::val& wnn_limits, const logging::Logger& logger) const;
+
+  const bool allow_empty_tensor_as_input_;  // Some operators can handle ignoring an empty tensor as input.
 };
 
 }  // namespace webnn
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 408045571e422..00f8cff25ccf5 100644
--- a/onnxruntime/core/providers/webnn/builders/impl/resize_op_builder.cc
+++ b/onnxruntime/core/providers/webnn/builders/impl/resize_op_builder.cc
@@ -21,6 +21,8 @@ namespace webnn {
 class ResizeOpBuilder : public BaseOpBuilder {
   // Add operator related.
  public:
+  // Allow roi and scales potentially being empty inputs that are ignored during processing.
+  ResizeOpBuilder() : BaseOpBuilder(/*allow empty inputs*/ true) {}
   void AddInitializersToSkip(ModelBuilder& model_builder, const Node& node) const override;
 
  private: