diff --git a/pyximport/pyximport.py b/pyximport/pyximport.py
index 629325933ec..96a727961d9 100644
--- a/pyximport/pyximport.py
+++ b/pyximport/pyximport.py
@@ -185,13 +185,13 @@ def build_module(name, pyxfilename, pyxbuild_dir=None, inplace=False, language_l
     from . import pyxbuild
     olddir = os.getcwd()
     common = ''
-    if pyxbuild_dir:
+    if pyxbuild_dir and sys.platform == 'win32':
         # Windows concatenates the pyxbuild_dir to the pyxfilename when
         # compiling, and then complains that the filename is too long
         common = os.path.commonprefix([pyxbuild_dir, pyxfilename])
     if len(common) > 30:
-        pyxfilename = os.path.relpath(pyxfilename)
-        pyxbuild_dir = os.path.relpath(pyxbuild_dir)
+        pyxfilename = os.path.relpath(pyxfilename, common)
+        pyxbuild_dir = os.path.relpath(pyxbuild_dir, common)
         os.chdir(common)
     try:
         so_path = pyxbuild.pyx_to_dll(pyxfilename, extension_mod,