diff --git a/src/meta_schedule/measure_callback/update_cost_model.cc b/src/meta_schedule/measure_callback/update_cost_model.cc
index 0563699ba6b9..8a8a43658409 100644
--- a/src/meta_schedule/measure_callback/update_cost_model.cc
+++ b/src/meta_schedule/measure_callback/update_cost_model.cc
@@ -42,7 +42,8 @@ class UpdateCostModelNode : public MeasureCallbackNode {
     pruned_candidate.reserve(n);
     pruned_runner_result.reserve(n);
     for (int i = 0; i < n; i++) {
-      if (!builder_results[i]->error_msg.defined()) {
+      if (!builder_results[i]->error_msg.defined() &&
+          Sum(runner_results[i]->run_secs.value()) > 0) {
         pruned_candidate.push_back(measure_candidates[i]);
         pruned_runner_result.push_back(runner_results[i]);
       }
diff --git a/src/meta_schedule/utils.h b/src/meta_schedule/utils.h
index 80264516c4ce..969aa630df39 100644
--- a/src/meta_schedule/utils.h
+++ b/src/meta_schedule/utils.h
@@ -540,6 +540,19 @@ inline ScheduleRule GetDefaultAutoInline(const std::string& target_name) {
   throw;
 }
 
+/*!
+ * \brief Summarize the run time of the given FloatImm array.
+ * \param arr The array of FloatImm.
+ * \return The summary of the values in the given array.
+ */
+inline double Sum(const Array<FloatImm>& arr) {
+  double sum = 0;
+  for (const FloatImm& f : arr) {
+    sum += f->value;
+  }
+  return sum;
+}
+
 }  // namespace meta_schedule
 }  // namespace tvm
 
diff --git a/tests/python/unittest/test_meta_schedule_measure_callback.py b/tests/python/unittest/test_meta_schedule_measure_callback.py
index 20596e8e8c4d..c3fbbbe97231 100644
--- a/tests/python/unittest/test_meta_schedule_measure_callback.py
+++ b/tests/python/unittest/test_meta_schedule_measure_callback.py
@@ -16,12 +16,12 @@
 # under the License.
 # pylint: disable=missing-module-docstring,missing-function-docstring,missing-class-docstring
 import re
+import tempfile
 from typing import List
 
 import pytest
 import tvm
 from tvm import meta_schedule as ms
-from tvm.meta_schedule.testing.dummy_object import DummyBuilder, DummyRunner
 from tvm.script import tir as T
 from tvm.tir.schedule import Schedule
 
@@ -123,7 +123,33 @@ def apply(
     assert pattern.match(str(measure_callback))
 
 
+def test_meta_schedule_measure_callback_update_cost_model_with_zero():
+    @ms.derived_object
+    class AllZeroRunnerFuture(ms.runner.PyRunnerFuture):
+        def done(self) -> bool:
+            return True
+
+        def result(self) -> ms.runner.RunnerResult:
+            return ms.runner.RunnerResult([0.0, 0.0], None)
+
+    @ms.derived_object
+    class AllZeroRunner(ms.runner.PyRunner):
+        def run(self, runner_inputs: List[ms.runner.RunnerInput]) -> List[ms.runner.RunnerResult]:
+            return [AllZeroRunnerFuture() for _ in runner_inputs]
+
+    with tempfile.TemporaryDirectory() as work_dir:
+        ms.tune_tir(
+            mod=Matmul,
+            target="llvm -num-cores=1",
+            work_dir=work_dir,
+            max_trials_global=10,
+            runner=AllZeroRunner(),
+            measure_callbacks=[ms.measure_callback.UpdateCostModel()],
+        )
+
+
 if __name__ == "__main__":
     test_meta_schedule_measure_callback()
     test_meta_schedule_measure_callback_fail()
     test_meta_schedule_measure_callback_as_string()
+    test_meta_schedule_measure_callback_update_cost_model_with_zero()