Since you're searching for a constant string, index is faster than a regexp:

foreach my $elem (@repos) {
   my $repo_name = $elem;

   my $pos = index(lc($repo_name), lc($svnroot));

   if ($pos >= 0) {
      substr($repo_name, $pos, length($svnroot), '');
   }

   print("$repo_name\n");
}
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Or since you probably meant to search for /^\Q$svnroot\E/ (i.e. search for $svnroot at the beginning of the string), this is more precise and even faster:

foreach my $elem (@repos) {
   if (lc($svnroot) eq substr(lc($elem), 0, length($svnroot))) {
      print(substr($elem, length($svnroot)), "\n");
   } else {
      print("$elem\n");
   }
}
[download]