Mackin signed for York permanently on 22 May 2009 on a one-year contract. After signing, manager Martin Foyle said "Levi was fantastic for us and came on in leaps and bounds. He was one of our most consistent players, but I know there's more to come from him." Mackin played in the opening match of 2009–10, a 2–1 defeat away to Oxford on 8 August 2009, and according to "The Press" was a "strong presence in the City midfield in a very committed performance". A foot infection led to him missing a match against Gateshead on 25 August 2009 and he made his return in a 2–0 home win over Crawley Town on 5 September as an 84th-minute substitute. His first start since 22 August 2009 came in a 2–2 home draw with Cambridge United on 22 September to fill in for Alex Lawless. This was the first of five consecutive matches to be started by Mackin before he had a six-match spell on the substitutes' bench. This came to an end when he started in the 1–0 victory away to AFC Wimbledon on 21 November 2009 and his performance drew praise from Foyle.