--- a/build/config/linux/pkg-config.py
+++ b/build/config/linux/pkg-config.py
@@ -96,8 +96,10 @@

 def RewritePath(path, strip_prefix, sysroot):
   """Rewrites a path by stripping the prefix and prepending the sysroot."""
   if os.path.isabs(path) and not path.startswith(sysroot):
-    if path.startswith(strip_prefix):
+    if strip_prefix and path.startswith(strip_prefix):
       path = path[len(strip_prefix):]
+    elif path != '/usr' and not path.startswith('/usr/'):
+      return path
     path = path.lstrip('/')
     return os.path.join(sysroot, path)