diff --git a/tools/counter/Makefile b/tools/counter/Makefile
index 8843f0fa6119..a0f4cab71fe5 100644
--- a/tools/counter/Makefile
+++ b/tools/counter/Makefile
@@ -40,6 +40,7 @@ $(OUTPUT)counter_example: $(COUNTER_EXAMPLE)
 clean:
 	rm -f $(ALL_PROGRAMS)
 	rm -rf $(OUTPUT)include/linux/counter.h
+	rmdir -p $(OUTPUT)include/linux
 	find $(or $(OUTPUT),.) -name '*.o' -delete -o -name '\.*.d' -delete
 
 install: $(ALL_PROGRAMS)