diff --git a/scripts/build-llvm-v5.sh b/scripts/build-llvm-v5.sh
index 2f53b3c..a5dfee1 100755
--- a/scripts/build-llvm-v5.sh
+++ b/scripts/build-llvm-v5.sh
@@ -164,6 +164,13 @@ done
 #     fi
 # done
 
+# Ensure clang runs with the correct GCC installation and the correct search dirs.
+CLANG_CFG=$PREFIX/clang.cfg
+CLANGXX_CFG=$PREFIX/clang++.cfg
+CLANG_CFG_FLAGS="--gcc-toolchain=$GCC_PREFIX"
+CLANGXX_CFG_FLAGS="$CLANG_CFG_FLAGS"
+echo "$CLANG_CFG_FLAGS" > $CLANG_CFG
+echo "$CLANGXX_CFG_FLAGS" > $CLANGXX_CFG
+
 invoke () {
     if [[ $1 == cmake ]]; then
         CMD="${CMAKE}"
@@ -211,6 +218,10 @@ MONGO_CMAKE_ARGS=(
     -DCMAKE_C_COMPILER="$GCC_PREFIX/bin/gcc"
     -DCMAKE_CXX_COMPILER="$GCC_PREFIX/bin/g++"
 
+    -DCLANG_CONFIG_FILE_SYSTEM_DIR=$PREFIX
+    -DCMAKE_EXE_LINKER_FLAGS="-Wl,-rpath,${GCC_PREFIX}/lib64 -Wl,-rpath,${GCC_PREFIX}/lib"
+    -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-rpath,${GCC_PREFIX}/lib64 -Wl,-rpath,${GCC_PREFIX}/lib"
+
     # TODO BUILD-16234
     # remove the RHEL6 support
     -DCMAKE_INCLUDE_PATH="$MONGO_CMAKE_INCLUDE_PATH"
@@ -317,7 +328,7 @@ time invoke ninja                        \
     stage2-install install-cmake-exports | tee build_output.txt
 
 grep -E -e "-c\s.*/clang-tools-extra/clang-tidy/ClangTidyModule\.cpp" build_output.txt | head -1 > raw_compile.txt
-grep -E -e "-o\sbin/clang-tidy" build_output.txt | head -1 > raw_link.txt
+grep -E -e "-o\sbin/clang-tidy\s" build_output.txt | head -1 > raw_link.txt
 $PYTHON3_PREFIX/bin/python3 $START_DIR/scripts/parse_clang_tidy_args.py --raw-compile-file=raw_compile.txt --raw-link-file=raw_link.txt
 mv clang_tidy_build_flags.json $PREFIX/bin/