The 2012–13 season was the 91st season of competitive association football and 76th season in the Football League played by York City Football Club, a professional football club based in York, North Yorkshire, England. Their promotion via the Conference Premier play-offs in 2011–12 meant they played in League Two, after an eight-year absence from the Football League. The season ran from 1 July 2012 to 30 June 2013.

Manager Gary Mills signed eight players before the close of the summer transfer window. Having stood 14th in the league table on New Year's Day, York were on an 11-match run without a win when Mills was sacked during March 2013. He was replaced by former Northern Ireland manager Nigel Worthington, who led York to safety from relegation on the final day of the season. Having won four of their last five matches, the team finished the season 17th in the table. They lost in their opening round matches in both the 2012–13 FA Cup and the League Cup, and were eliminated in the second round of the Football League Trophy.

36 players made at least one appearance in nationally organised first-team competition, and there were 12 different goalscorers. Goalkeeper Michael Ingham played in all 50 first-team matches over the season. Ashley Chambers finished as leading scorer with 10 goals, all scored in the league. The winner of the Clubman of the Year award, voted for by the club's supporters, was Danny Parslow, who became the first player to win the award for a third time.

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