With a compensation package agreed Mills left Tamworth after being appointed the manager of fellow Conference Premier club York City on 13 October 2010. He replaced Martin Foyle, who resigned the previous month, and at the time of his appointment York were 16th in the table. He was not registered as a player at York, although chairman Jason McGill would refuse Mills a playing contract on multiple occasions. After his appointment, Mills said he believed he had left Tamworth for a club with greater potential and that his aim was to return York to the Football League.