Index: CMakeLists.txt
===================================================================
--- CMakeLists.txt
+++ CMakeLists.txt
@@ -615,9 +615,10 @@
   config_define(ON _LIBCPP_DISABLE_VISIBILITY_ANNOTATIONS)
 endif()
 
+set(site_config_path "${LIBCXX_BINARY_DIR}/__config_site")
 if (LIBCXX_NEEDS_SITE_CONFIG)
   configure_file("include/__config_site.in"
-                 "${LIBCXX_BINARY_DIR}/__config_site"
+                 "${site_config_path}"
                  @ONLY)
 
   # Provide the config definitions by included the generated __config_site
@@ -627,6 +628,10 @@
   else()
     add_compile_flags("-include ${LIBCXX_BINARY_DIR}/__config_site")
   endif()
+else()
+  if (EXISTS "${site_config_path}")
+    file(REMOVE "${site_config_path}")
+  endif()
 endif()
 
 #===============================================================================