diff --git a/python/educational-python/src/com/jetbrains/python/edu/debugger/PyEduConsoleInputFilterProvider.java b/python/educational-python/src/com/jetbrains/python/edu/debugger/PyEduConsoleInputFilterProvider.java
index 0f74c0277511..1f191c949548 100644
--- a/python/educational-python/src/com/jetbrains/python/edu/debugger/PyEduConsoleInputFilterProvider.java
+++ b/python/educational-python/src/com/jetbrains/python/edu/debugger/PyEduConsoleInputFilterProvider.java
@@ -5,6 +5,7 @@ import com.intellij.execution.filters.InputFilter;
 import com.intellij.execution.ui.ConsoleViewContentType;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.util.Pair;
+import com.jetbrains.python.debugger.PyRunCythonExtensionsFilter;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 
@@ -22,6 +23,9 @@ public class PyEduConsoleInputFilterProvider implements ConsoleInputFilterProvid
         if (outputType.equals(ConsoleViewContentType.SYSTEM_OUTPUT) && !text.contains("exit code")) {
           return Collections.emptyList();
         }
+        if (text.startsWith(PyRunCythonExtensionsFilter.WARNING_MESSAGE_BEGIN)) {
+          return Collections.emptyList();
+        }
         if (text.startsWith("pydev debugger")) {
           return Collections.emptyList();
         }