diff --git a/onnxruntime/core/providers/cpu/nn/pool_attributes.h b/onnxruntime/core/providers/cpu/nn/pool_attributes.h
index 118cb4a3ba..fbbd427375 100644
--- a/onnxruntime/core/providers/cpu/nn/pool_attributes.h
+++ b/onnxruntime/core/providers/cpu/nn/pool_attributes.h
@@ -150,14 +150,14 @@ struct PoolAttributes {
         case AutoPadType::VALID:
           *pad_head = 0;
           *pad_tail = 0;
-          *out_size = ComputeOutputSize(in_size, stride, kernel, 0, dilation);
+          *out_size = ComputeOutputSize(in_size, stride, kernel, 0, 0, dilation);
           break;
         case AutoPadType::SAME_LOWER: {
           int64_t legacy_target_size = (in_size + stride - 1) / stride;
           int64_t pad_needed = (legacy_target_size - 1) * stride + kernel - in_size;
           *pad_head = (pad_needed + 1) / 2;
           *pad_tail = pad_needed - *pad_head;
-          *out_size = ComputeOutputSize(in_size, stride, kernel, pad_needed, dilation);
+          *out_size = ComputeOutputSize(in_size, stride, kernel, *pad_head, *pad_tail, dilation);
           break;
         }
         case AutoPadType::SAME_UPPER: {
@@ -165,7 +165,7 @@ struct PoolAttributes {
           int64_t pad_needed = (legacy_target_size - 1) * stride + kernel - in_size;
           *pad_head = pad_needed / 2;
           *pad_tail = pad_needed - *pad_head;
-          *out_size = ComputeOutputSize(in_size, stride, kernel, pad_needed, dilation);
+          *out_size = ComputeOutputSize(in_size, stride, kernel, *pad_head, *pad_tail, dilation);
           break;
         }
         default: {
@@ -173,7 +173,7 @@ struct PoolAttributes {
         }
       }
     } else {
-      *out_size = ComputeOutputSize(in_size, stride, kernel, *pad_head + *pad_tail, dilation);
+      *out_size = ComputeOutputSize(in_size, stride, kernel, *pad_head, *pad_tail, dilation);
     }
   }
 #if defined(_MSC_VER) && !defined(__clang__)
@@ -184,13 +184,21 @@ struct PoolAttributes {
   int64_t ComputeOutputSize(int64_t in_size,
                             int64_t stride,
                             int64_t kernel,
-                            int64_t pad_needed,
+                            int64_t pad_head,
+                            int64_t pad_tail,
                             int64_t dilation) const {
-    if (ceil_mode == 0) {
-      return static_cast<int64_t>(static_cast<float>(in_size + pad_needed - dilation * (kernel - 1) - 1) / stride + 1);
+    int64_t numerator = in_size + pad_head + pad_tail - dilation * (kernel - 1) - 1;
+    int64_t out_size = numerator / stride + 1;
+
+    if (ceil_mode == 1) {
+      out_size = static_cast<int64_t>(std::ceil(static_cast<float>(numerator) / stride)) + 1;
+      // Ensure that the last pooling starts inside the image (at least 1 pixel)
+      // Reference: https://github.com/onnx/onnx/pull/5741
+      if ((out_size - 1) * stride >= in_size + pad_head) {
+        --out_size;
+      }
     }
-    return static_cast<int64_t>(
-        std::ceil(static_cast<float>(in_size + pad_needed - dilation * (kernel - 1) - 1) / stride + 1));
+    return out_size;
   }
 #if defined(_MSC_VER) && !defined(__clang__)
 #pragma warning(pop)
diff --git a/onnxruntime/core/providers/cpu/nn/pool_functors.h b/onnxruntime/core/providers/cpu/nn/pool_functors.h
index d3205278b7..476a9a0338 100644
--- a/onnxruntime/core/providers/cpu/nn/pool_functors.h
+++ b/onnxruntime/core/providers/cpu/nn/pool_functors.h
@@ -406,6 +406,7 @@ struct AveragePool1DTask final {
     for (int64_t ph = 0; ph < pooled_height; ++ph) {
       int64_t hstart = ph * stride_h - pads[0];
       int64_t hend = hstart + kernel_shape[0] * dilation_h;
+      hend = std::min(hend, height + pads[1]);
       y_d[ph] = 0;
       int total_elements = 0;
       for (int64_t h = hstart; h < hend; h += dilation_h) {
@@ -461,9 +462,11 @@ struct AveragePool2DTask final {
     for (int64_t ph = 0; ph < pooled_height; ++ph) {
       int64_t hstart = ph * stride_h - pads[0];
       int64_t hend = hstart + kernel_shape[0] * dilation_h;
+      hend = std::min(hend, height + pads[1]);
       for (int64_t pw = 0; pw < pooled_width; ++pw) {
         int64_t wstart = pw * stride_w - pads[1];
         int64_t wend = wstart + kernel_shape[1] * dilation_w;
+        wend = std::min(wend, width + pads[3]);
         const int64_t pool_index = ph * pooled_width + pw;
         y_d[pool_index] = 0;
         int total_elements = 0;
@@ -532,12 +535,15 @@ struct AveragePool3DTask {
     for (int64_t ph = 0; ph < pooled_height; ++ph) {
       int64_t hstart = ph * stride_h - pads[0];
       int64_t hend = hstart + kernel_shape[0] * dilation_h;
+      hend = std::min(hend, height + pads[1]);
       for (int64_t pw = 0; pw < pooled_width; ++pw) {
         int64_t wstart = pw * stride_w - pads[1];
         int64_t wend = wstart + kernel_shape[1] * dilation_w;
+        wend = std::min(wend, width + pads[3]);
         for (int64_t pd = 0; pd < pooled_depth; ++pd) {
           int64_t dstart = pd * stride_d - pads[2];
           int64_t dend = dstart + kernel_shape[2] * dilation_d;
+          dend = std::min(dend, depth + pads[5]);
           const int64_t pool_index = ph * pooled_width * pooled_depth + pw * pooled_depth + pd;
           y_d[pool_index] = 0;
           int total_elements = 0;
diff --git a/onnxruntime/test/onnx/TestCase.cc b/onnxruntime/test/onnx/TestCase.cc
index b9b69fdc74..d44f098db6 100644
--- a/onnxruntime/test/onnx/TestCase.cc
+++ b/onnxruntime/test/onnx/TestCase.cc
@@ -961,6 +961,7 @@ std::unique_ptr<std::set<BrokenTest>> GetBrokenTests(const std::string& provider
       {"reduce_prod_empty_set", "unknown version", {}},
       {"reduce_sum_empty_set", "unknown version", {}},
       {"reduce_sum_square_empty_set_expanded", "unknown version", {}},
+      {"averagepool_3d_dilations_large_count_include_pad_is_1_ceil_mode_is_True", "TODO(titaiwang): enable this in the next ONNX release."},
 #ifdef ENABLE_TRAINING_CORE
       {"adagrad", "not a registered function/op", {}},                  // Op not registered.
       {"adagrad_multiple", "not a registered function/op", {}},         // Op not registered.
diff --git a/onnxruntime/test/providers/cpu/nn/pool_op_test.cc b/onnxruntime/test/providers/cpu/nn/pool_op_test.cc
index a340f975ec..24a8c8491b 100644
--- a/onnxruntime/test/providers/cpu/nn/pool_op_test.cc
+++ b/onnxruntime/test/providers/cpu/nn/pool_op_test.cc
@@ -1030,6 +1030,31 @@ TEST(PoolTest, AveragePool_19_dilation_2d) {
             kTensorrtExecutionProvider, kAclExecutionProvider, kOpenVINOExecutionProvider});
 }
 
+TEST(PoolTest, AveragePool_19_ceil_count_include_pad_1d) {
+  // TODO: Unskip when fixed #41968513
+  if (DefaultDmlExecutionProvider().get() != nullptr) {
+    GTEST_SKIP() << "Skipping because of the following error: MLOperatorAuthorImpl.cpp(2100): The parameter is incorrect.";
+  }
+
+  OpTester test("AveragePool", 19);
+
+  test.AddAttribute("auto_pad", "");
+  test.AddAttribute("strides", std::vector<int64_t>{3});
+  test.AddAttribute("pads", vector<int64_t>{3, 3});
+  test.AddAttribute("kernel_shape", vector<int64_t>{7});
+  test.AddAttribute("ceil_mode", (int64_t)1);
+  test.AddAttribute("count_include_pad", (int64_t)1);
+
+  std::vector<float> x_vals = {2.0903f, 4.6493f, 1.6320f, -3.2051f, 4.6975f, 4.7296f, 3.3653f, -1.5815f, -2.3832f, 0.9628f, -1.5899f, -2.6820f, 5.7529f, 7.7346f, -0.8910f, -2.0151f, 0.1313f, -0.5374f};
+  std::vector<int64_t> x_dims = {1, 2, 9};
+  std::vector<int64_t> expected_dims = {1, 2, 4};
+  std::vector<float> expected_vals = {0.73807144f, 2.5655572f, 0.8032287f, -0.09990001f, 0.34911433f, 1.0389f, 1.4536142f, -0.40353334f};
+
+  test.AddInput<float>("X", x_dims, x_vals);
+  test.AddOutput<float>("Y", expected_dims, expected_vals);
+  test.Run(OpTester::ExpectResult::kExpectSuccess, "", {kTensorrtExecutionProvider, kAclExecutionProvider, kOpenVINOExecutionProvider});
+}
+
 TEST(PoolTest, GlobalAveragePool) {
   OpTester test("GlobalAveragePool");