diff --git a/src/e-sync.js b/src/e-sync.js
index 7d8d85df..3ec043bb 100644
--- a/src/e-sync.js
+++ b/src/e-sync.js
@@ -18,7 +18,9 @@ function setRemotes(cwd, repo) {
       .trim(),
   );
 
-  if (gitRoot !== cwd) {
+  // Check if the directories are the same in a way that handles case-insensitive
+  // filesystems
+  if (path.relative(gitRoot, cwd) !== '') {
     fatal(`Expected git root to be ${cwd} but found ${gitRoot}`);
   }