His first appearance of 2006–07 was in a 0–0 home draw with Peterborough United on 12 August 2006, a match he entered as a 59th-minute substitute. The next game he played in was a 4–1 victory away to Championship team Sheffield Wednesday in the League Cup on 23 August 2006. Mackin suffered a knee injury during a reserve-team match in September 2006 and made his return as a 90th-minute substitute in a 4–1 defeat after extra time away to Birmingham City of the Championship in the League Cup second round on 19 September. He picked up another knee injury in October 2006 and made his return in a 2–1 defeat at home to MK Dons on 14 October. An injury to Mark Jones allowed Mackin back into the team for a 4–0 defeat away to Boston United on 9 December 2006. His 2006–07 season finished with 11 appearances as opportunities in the team were "frustratingly rare" and he was offered a new long-term contract by Wrexham in May 2007.