diff --git a/onnxruntime/core/providers/cpu/ml/tree_ensemble_aggregator.h b/onnxruntime/core/providers/cpu/ml/tree_ensemble_aggregator.h
index 3b7eb82294761..ebdac882bff09 100644
--- a/onnxruntime/core/providers/cpu/ml/tree_ensemble_aggregator.h
+++ b/onnxruntime/core/providers/cpu/ml/tree_ensemble_aggregator.h
@@ -480,6 +480,7 @@ class TreeAggregatorClassifier : public TreeAggregatorSum<InputType, ThresholdTy
  private:
   const std::vector<int64_t>& class_labels_;
   bool binary_case_;
+  bool weights_are_all_positive_;
   int64_t positive_label_;
   int64_t negative_label_;
 
@@ -490,11 +491,13 @@ class TreeAggregatorClassifier : public TreeAggregatorSum<InputType, ThresholdTy
                            const std::vector<ThresholdType>& base_values,
                            const std::vector<int64_t>& class_labels,
                            bool binary_case,
+                           bool weights_are_all_positive,
                            int64_t positive_label = 1,
                            int64_t negative_label = 0) : TreeAggregatorSum<InputType, ThresholdType, OutputType>(n_trees, n_targets_or_classes,
                                                                                                                  post_transform, base_values),
                                                          class_labels_(class_labels),
                                                          binary_case_(binary_case),
+                                                         weights_are_all_positive_(weights_are_all_positive),
                                                          positive_label_(positive_label),
                                                          negative_label_(negative_label) {}
 
@@ -523,12 +526,22 @@ class TreeAggregatorClassifier : public TreeAggregatorSum<InputType, ThresholdTy
                             ThresholdType score1, unsigned char has_score1) const {
     ThresholdType pos_weight = has_score1 ? score1 : (has_score0 ? score0 : 0);  // only 1 class
     if (binary_case_) {
-      if (pos_weight > 0) {
-        write_additional_scores = 2;
-        return class_labels_[1];  // positive label
+      if (weights_are_all_positive_) {
+        if (pos_weight > 0.5) {
+          write_additional_scores = 0;
+          return class_labels_[1];  // positive label
+        } else {
+          write_additional_scores = 1;
+          return class_labels_[0];  // negative label
+        }
       } else {
-        write_additional_scores = 3;
-        return class_labels_[0];  // negative label
+        if (pos_weight > 0) {
+          write_additional_scores = 2;
+          return class_labels_[1];  // positive label
+        } else {
+          write_additional_scores = 3;
+          return class_labels_[0];  // negative label
+        }
       }
     }
     return (pos_weight > 0)
diff --git a/onnxruntime/core/providers/cpu/ml/tree_ensemble_common.h b/onnxruntime/core/providers/cpu/ml/tree_ensemble_common.h
index 96a237f9dbf75..7ea9cc1edc478 100644
--- a/onnxruntime/core/providers/cpu/ml/tree_ensemble_common.h
+++ b/onnxruntime/core/providers/cpu/ml/tree_ensemble_common.h
@@ -983,6 +983,7 @@ TreeEnsembleCommon<InputType, ThresholdType, OutputType>::ProcessTreeNodeLeave(
 template <typename InputType, typename ThresholdType, typename OutputType>
 class TreeEnsembleCommonClassifier : public TreeEnsembleCommon<InputType, ThresholdType, OutputType> {
  private:
+  bool weights_are_all_positive_;
   bool binary_case_;
   std::vector<std::string> classlabels_strings_;
   std::vector<int64_t> classlabels_int64s_;
@@ -1018,7 +1019,15 @@ Status TreeEnsembleCommonClassifier<InputType, ThresholdType, OutputType>::Init(
 
   InlinedHashSet<int64_t> weights_classes;
   weights_classes.reserve(attributes.target_class_ids.size());
-  weights_classes.insert(attributes.target_class_ids.begin(), attributes.target_class_ids.end());
+  weights_are_all_positive_ = true;
+  for (size_t i = 0, end = attributes.target_class_ids.size(); i < end; ++i) {
+    weights_classes.insert(attributes.target_class_ids[i]);
+    if (weights_are_all_positive_ && (attributes.target_class_weights_as_tensor.empty()
+                                          ? static_cast<ThresholdType>(attributes.target_class_weights[i])
+                                          : attributes.target_class_weights_as_tensor[i]) < 0) {
+      weights_are_all_positive_ = false;
+    }
+  }
   binary_case_ = this->n_targets_or_classes_ == 2 && weights_classes.size() == 1;
   if (!classlabels_strings_.empty()) {
     class_labels_.reserve(classlabels_strings_.size());
@@ -1039,7 +1048,8 @@ Status TreeEnsembleCommonClassifier<InputType, ThresholdType, OutputType>::compu
         TreeAggregatorClassifier<InputType, ThresholdType, OutputType>(
             this->roots_.size(), this->n_targets_or_classes_,
             this->post_transform_, this->base_values_,
-            classlabels_int64s_, binary_case_));
+            classlabels_int64s_, binary_case_,
+            weights_are_all_positive_));
   } else {
     int64_t N = X->Shape().NumDimensions() == 1 ? 1 : X->Shape()[0];
     AllocatorPtr alloc;
@@ -1050,7 +1060,8 @@ Status TreeEnsembleCommonClassifier<InputType, ThresholdType, OutputType>::compu
         TreeAggregatorClassifier<InputType, ThresholdType, OutputType>(
             this->roots_.size(), this->n_targets_or_classes_,
             this->post_transform_, this->base_values_,
-            class_labels_, binary_case_));
+            class_labels_, binary_case_,
+            weights_are_all_positive_));
     const int64_t* plabel = label_int64.Data<int64_t>();
     std::string* labels = label->MutableData<std::string>();
     for (size_t i = 0; i < (size_t)N; ++i)
diff --git a/onnxruntime/test/providers/cpu/ml/tree_ensembler_classifier_test.cc b/onnxruntime/test/providers/cpu/ml/tree_ensembler_classifier_test.cc
index df97056284ae7..4a56579bcfca1 100644
--- a/onnxruntime/test/providers/cpu/ml/tree_ensembler_classifier_test.cc
+++ b/onnxruntime/test/providers/cpu/ml/tree_ensembler_classifier_test.cc
@@ -709,5 +709,115 @@ TEST(MLOpTest, TreeEnsembleNegativeFeatureIds) {
   test.Run(OpTester::ExpectResult::kExpectFailure, "nodes_featureids[0]=-2 must be in [0, 2147483647] for non-leaf nodes");
 }
 
+// Regression test for PR #27552 which inadvertently broke binary TreeEnsembleClassifier models
+// with all-positive weights and non-LOGISTIC post_transform (e.g., sklearn RandomForestClassifier).
+// When weights are all non-negative (probability-like values in [0,1]), the threshold for the
+// positive class should be > 0.5 and the complement should be computed as 1-score (not -score).
+// Without the weights_are_all_positive_ flag, scores in (0, 0.5) would produce negative
+// "probabilities" and incorrect labels.
+TEST(MLOpTest, TreeEnsembleClassifierBinaryAllPositiveWeightsNone) {
+  // 3 trees, each with a root branching on feature 0 at threshold 0.5.
+  // Left leaf (feature <= 0.5): weight = 0.2 (low probability for class 1)
+  // Right leaf (feature > 0.5): weight = 0.8 (high probability for class 1)
+  //
+  // For input x=0.0: all 3 trees go left, avg score = 0.2 (< 0.5 → label 0)
+  // For input x=1.0: all 3 trees go right, avg score = 0.8 (> 0.5 → label 1)
+  // For input x=0.0 with 1 tree going right: score = (0.2+0.2+0.8)/3 ≈ 0.4 (< 0.5 → label 0)
+  //
+  // Binary case: classlabels_int64s={0,1}, class_ids all 0, all weights in [0,1].
+  // post_transform = NONE (default).
+
+  // Single tree for simplicity: root → left leaf (weight 0.3) or right leaf (weight 0.8)
+  std::vector<int64_t> treeids = {0, 0, 0};
+  std::vector<int64_t> nodeids = {0, 1, 2};
+  std::vector<int64_t> featureids = {0, -2, -2};
+  std::vector<float> thresholds = {0.5f, -2.f, -2.f};
+  std::vector<std::string> modes = {"BRANCH_LEQ", "LEAF", "LEAF"};
+  std::vector<int64_t> truenodeids = {1, -1, -1};
+  std::vector<int64_t> falsenodeids = {2, -1, -1};
+
+  // Both leaves target class 0 (single-column binary encoding).
+  // All weights are positive — this triggers weights_are_all_positive_=true.
+  std::vector<int64_t> class_treeids = {0, 0};
+  std::vector<int64_t> class_nodeids = {1, 2};
+  std::vector<int64_t> class_classids = {0, 0};
+  std::vector<float> class_weights = {0.3f, 0.8f};
+  std::vector<int64_t> classes = {0, 1};
+
+  // Test 1: score = 0.3 (< 0.5) → label should be 0, probabilities should be [0.7, 0.3]
+  {
+    OpTester test("TreeEnsembleClassifier", 1, onnxruntime::kMLDomain);
+    test.AddAttribute("nodes_treeids", treeids);
+    test.AddAttribute("nodes_nodeids", nodeids);
+    test.AddAttribute("nodes_featureids", featureids);
+    test.AddAttribute("nodes_values", thresholds);
+    test.AddAttribute("nodes_modes", modes);
+    test.AddAttribute("nodes_truenodeids", truenodeids);
+    test.AddAttribute("nodes_falsenodeids", falsenodeids);
+    test.AddAttribute("class_treeids", class_treeids);
+    test.AddAttribute("class_nodeids", class_nodeids);
+    test.AddAttribute("class_ids", class_classids);
+    test.AddAttribute("class_weights", class_weights);
+    test.AddAttribute("classlabels_int64s", classes);
+
+    // x=0.0 → goes left (0.0 <= 0.5) → leaf 1, weight = 0.3
+    test.AddInput<float>("X", {1, 1}, {0.0f});
+    test.AddOutput<int64_t>("Y", {1}, {0});
+    // write_additional_scores=1: complement = 1-score → [1-0.3, 0.3] = [0.7, 0.3]
+    test.AddOutput<float>("Z", {1, 2}, {0.7f, 0.3f});
+    test.Run();
+  }
+
+  // Test 2: score = 0.8 (> 0.5) → label should be 1, probabilities should be [0.2, 0.8]
+  {
+    OpTester test("TreeEnsembleClassifier", 1, onnxruntime::kMLDomain);
+    test.AddAttribute("nodes_treeids", treeids);
+    test.AddAttribute("nodes_nodeids", nodeids);
+    test.AddAttribute("nodes_featureids", featureids);
+    test.AddAttribute("nodes_values", thresholds);
+    test.AddAttribute("nodes_modes", modes);
+    test.AddAttribute("nodes_truenodeids", truenodeids);
+    test.AddAttribute("nodes_falsenodeids", falsenodeids);
+    test.AddAttribute("class_treeids", class_treeids);
+    test.AddAttribute("class_nodeids", class_nodeids);
+    test.AddAttribute("class_ids", class_classids);
+    test.AddAttribute("class_weights", class_weights);
+    test.AddAttribute("classlabels_int64s", classes);
+
+    // x=1.0 → goes right (1.0 > 0.5) → leaf 2, weight = 0.8
+    test.AddInput<float>("X", {1, 1}, {1.0f});
+    test.AddOutput<int64_t>("Y", {1}, {1});
+    // write_additional_scores=0: complement = 1-score → [1-0.8, 0.8] = [0.2, 0.8]
+    test.AddOutput<float>("Z", {1, 2}, {0.2f, 0.8f});
+    test.Run();
+  }
+
+  // Test 3: score = 0.5 (boundary, <= 0.5) → label should be 0
+  {
+    OpTester test("TreeEnsembleClassifier", 1, onnxruntime::kMLDomain);
+    // Use weight = 0.5 for the left leaf to test the boundary
+    std::vector<float> boundary_weights = {0.5f, 0.8f};
+    test.AddAttribute("nodes_treeids", treeids);
+    test.AddAttribute("nodes_nodeids", nodeids);
+    test.AddAttribute("nodes_featureids", featureids);
+    test.AddAttribute("nodes_values", thresholds);
+    test.AddAttribute("nodes_modes", modes);
+    test.AddAttribute("nodes_truenodeids", truenodeids);
+    test.AddAttribute("nodes_falsenodeids", falsenodeids);
+    test.AddAttribute("class_treeids", class_treeids);
+    test.AddAttribute("class_nodeids", class_nodeids);
+    test.AddAttribute("class_ids", class_classids);
+    test.AddAttribute("class_weights", boundary_weights);
+    test.AddAttribute("classlabels_int64s", classes);
+
+    // x=0.0 → leaf 1, weight = 0.5 (not > 0.5, so label = 0)
+    test.AddInput<float>("X", {1, 1}, {0.0f});
+    test.AddOutput<int64_t>("Y", {1}, {0});
+    // write_additional_scores=1: [1-0.5, 0.5] = [0.5, 0.5]
+    test.AddOutput<float>("Z", {1, 2}, {0.5f, 0.5f});
+    test.Run();
+  }
+}
+
 }  // namespace test
 }  // namespace onnxruntime