 Mills was unable to keep York City in the National League and they were Relegated to the National League North on 29 April 2017 after a 2–2 draw with Forest Green Rovers.However, on 21 May 2017, Mills' York beat Macclesfield Town 3–2 at Wembley Stadium in the 2017 FA Trophy Final.Mills was dismissed by York on 30 September 2017, on the same day as a defeat to South Shields in the FA Cup third qualifying round.