diff --git a/include/treelite/model_builder.h b/include/treelite/model_builder.h
index 09c48c89..705bb5b4 100644
--- a/include/treelite/model_builder.h
+++ b/include/treelite/model_builder.h
@@ -39,6 +39,13 @@ class PostProcessorFunc;
  */
 class ModelBuilder {
  public:
+  /*!
+   * \brief Set a flag to control validation behavior.
+   * Currently, we support "check_orphaned_nodes" (defaults to true).
+   * \param flag Name of the flag
+   * \param value Value to set the flag
+   */
+  virtual void SetValidationFlag(std::string const& flag, bool value) = 0;
   /*!
    * \brief Start a new tree
    */
diff --git a/src/model_builder/model_builder.cc b/src/model_builder/model_builder.cc
index b7c2e6ba..5e77c628 100644
--- a/src/model_builder/model_builder.cc
+++ b/src/model_builder/model_builder.cc
@@ -66,7 +66,8 @@ class ModelBuilderImpl : public ModelBuilder {
         current_node_key_{},
         current_node_id_{},
         current_state_{ModelBuilderState::kExpectTree},
-        metadata_initialized_{false} {}
+        metadata_initialized_{false},
+        flag_check_orphaned_nodes_{true} {}
 
   ModelBuilderImpl(Metadata const& metadata, TreeAnnotation const& tree_annotation,
       PostProcessorFunc const& postprocessor, std::vector<double> const& base_scores,
@@ -79,10 +80,17 @@ class ModelBuilderImpl : public ModelBuilder {
         current_node_key_{},
         current_node_id_{},
         current_state_{ModelBuilderState::kExpectTree},
-        metadata_initialized_{false} {
+        metadata_initialized_{false},
+        flag_check_orphaned_nodes_{true} {
     InitializeMetadataImpl(metadata, tree_annotation, postprocessor, base_scores, attributes);
   }
 
+  void SetValidationFlag(std::string const& flag, bool value) override {
+    if (flag == "check_orphaned_nodes") {
+      flag_check_orphaned_nodes_ = value;
+    }
+  }
+
   void StartTree() override {
     CheckStateWithDiagnostic("StartTree()", {ModelBuilderState::kExpectTree}, current_state_);
 
@@ -121,17 +129,19 @@ class ModelBuilderImpl : public ModelBuilder {
         orphaned[cright] = false;
       }
     }
-    auto itr = std::find(orphaned.begin(), orphaned.end(), true);
-    if (itr != orphaned.end()) {
-      auto orphaned_node_id = *itr;
-      for (auto [k, v] : node_id_map_) {
-        if (v == orphaned_node_id) {
-          TREELITE_LOG(FATAL) << "Node with key " << k << " is orphaned -- it cannot be reached "
-                              << "from the root node";
+    if (flag_check_orphaned_nodes_) {
+      auto itr = std::find(orphaned.begin(), orphaned.end(), true);
+      if (itr != orphaned.end()) {
+        auto orphaned_node_id = *itr;
+        for (auto [k, v] : node_id_map_) {
+          if (v == orphaned_node_id) {
+            TREELITE_LOG(FATAL) << "Node with key " << k << " is orphaned -- it cannot be reached "
+                                << "from the root node";
+          }
         }
+        TREELITE_LOG(FATAL) << "Node at index " << orphaned_node_id << " is orphaned "
+                            << "-- it cannot be reached from the root node";
       }
-      TREELITE_LOG(FATAL) << "Node at index " << orphaned_node_id << " is orphaned "
-                          << "-- it cannot be reached from the root node";
     }
 
     auto& trees = std::get<ModelPreset<ThresholdT, LeafOutputT>>(model_->variant_).trees;
@@ -292,6 +302,7 @@ class ModelBuilderImpl : public ModelBuilder {
   int current_node_id_;  // current node ID (internal)
   ModelBuilderState current_state_;
   bool metadata_initialized_{false};
+  bool flag_check_orphaned_nodes_{true};
 
   void CheckStateWithDiagnostic(std::string const& func_name,
       std::vector<ModelBuilderState> const& valid_states, ModelBuilderState actual_state) {
diff --git a/src/model_loader/xgboost_json.cc b/src/model_loader/xgboost_json.cc
index ba8537f5..2ef8879a 100644
--- a/src/model_loader/xgboost_json.cc
+++ b/src/model_loader/xgboost_json.cc
@@ -377,6 +377,7 @@ bool GBTreeModelHandler::StartArray() {
   if (this->should_ignore_upcoming_value()) {
     return push_handler<IgnoreHandler>();
   }
+  output.builder->SetValidationFlag("check_orphaned_nodes", false);
   return (push_key_handler<RegTreeArrayHandler, std::vector<ParsedRegTreeParams>>(
               "trees", reg_tree_params, *output.builder)
           || push_key_handler<ArrayHandler<int>, std::vector<int>>("tree_info", output.tree_info)