diff --git a/tests/core/thread_flags/Makefile b/tests/core/thread_flags/Makefile
index 4c4170d48f..251db254d0 100644
--- a/tests/core/thread_flags/Makefile
+++ b/tests/core/thread_flags/Makefile
@@ -6,4 +6,7 @@ USEMODULE += xtimer
 # microbit qemu timing is off
 TEST_ON_CI_BLACKLIST += microbit
 
+# This test randomly fails on `native` so disable it from CI
+TEST_ON_CI_BLACKLIST += native native64
+
 include $(RIOTBASE)/Makefile.include