diff --git a/script/prepare-llvm-linux.sh b/script/prepare-llvm-linux.sh
index 7210b3cc8f..a261d3eac2 100755
--- a/script/prepare-llvm-linux.sh
+++ b/script/prepare-llvm-linux.sh
@@ -35,7 +35,7 @@ for f in $GLIBC/lib/lib{c,dl,m,rt,pthread}-*; do b=$(basename $f); cp $f stage1/
 OPTIONS=()
 echo -n " -DLEAN_STANDALONE=ON"
 echo -n " -DCMAKE_CXX_COMPILER=$PWD/llvm/bin/clang++ -DLEAN_CXX_STDLIB='-Wl,-Bstatic -lc++ -lc++abi -Wl,-Bdynamic'"
-echo -n " -DLEAN_EXTRA_CXX_FLAGS='--sysroot $PWD/llvm -isystem $GLIBC_DEV/include'"
+echo -n " -DLEAN_EXTRA_CXX_FLAGS='--sysroot $PWD/llvm -idirafter $GLIBC_DEV/include'"
 echo -n " -DCMAKE_C_COMPILER=$PWD/stage1/bin/clang"
 # use `-nostdinc` to make sure headers are not visible by default (in particular, not to `#include_next` in the clang headers),
 # but do not change sysroot so users can still link against system libs