diff --git a/libc/include/CMakeLists.txt b/libc/include/CMakeLists.txt
--- a/libc/include/CMakeLists.txt
+++ b/libc/include/CMakeLists.txt
@@ -511,6 +511,11 @@
   endif()
   file(RELATIVE_PATH relative_path ${LIBC_INCLUDE_BINARY_DIR} ${header_file})
   get_filename_component(nested_dir ${relative_path} DIRECTORY)
+  # The GPU headers are installed to 'gpu-none-llvm/' to prevent shadowing the
+  # system headers.
+  if(LIBC_TARGET_ARCHITECTURE_IS_GPU)
+    set(nested_dir gpu-none-llvm/${nested_dir})
+  endif()
   install(FILES ${header_file}
           DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/${nested_dir}
           COMPONENT libc-headers)