The 2008–09 season was the eighty-seventh season of competitive association football and fifth season in the Football Conference played by York City Football Club, a professional football club based in York, North Yorkshire, England. Their fourteenth-place finish in 2007–08 meant it was their fifth successive season in the Conference Premier. The season covers the period from 1 July 2008 to 30 June 2009.

Ahead of Colin Walker's first start to a season as manager, York signed nine players before the summer transfer window closed. The season started with an eight-match unbeaten run, but Walker was sacked in November 2008 after three successive defeats. Martin Foyle was appointed as his successor, and after the turn of the year York won only five league matches. Survival in the Conference Premier was achieved with a seventeenth-place finish. York reached the 2009 FA Trophy Final at Wembley Stadium, being beaten 2–0 by Stevenage Borough. They were eliminated from the 2008–09 FA Cup in the fourth qualifying round, and from the 2008–09 Conference League Cup in the Northern section fourth round.

Thirty-three players made at least one appearance in nationally organised first-team competition, and there were fourteen different goalscorers. Defender Danny Parslow missed only one of the fifty-eight competitive matches played over the season. Richard Brodie finished as leading scorer with nineteen goals, of which fifteen came in league competition and four came in the FA Trophy. The winner of the Clubman of the Year award, voted for by the club's supporters, was Parslow.

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