He was offered a new twelve-month contract by Stockport, but the first half of his 2008–09 season also turned out to be plagued by injury. After being sent off shortly into the second match of the season, McNeil suffered a knee injury in training, and missed the remainder of August, all of September, and the first half of October. He returned to face Colchester United on 18 October, scoring in the first half, but being hospitalised with a head injury by a clumsy challenge in the second half. After a further month out through injury, McNeil returned to the first team for a spell of games in November, before a recurrence of a back problem forced him to limp out of the pre-match warmup for an FA Cup tie against Gillingham on 9 December, and spend the next six weeks on the sidelines. McNeil was out of contract at the end of the season, and with the club going into administration, plus the management being made redundant, he wasn't offered a new contract.