The 2006–07 season was the eighty-fifth season of competitive association football and third season in the Football Conference played by York City F.C., an English football club based in York, North Yorkshire. They finished in fourth place in the twenty-four-team 2006–07 Conference National, qualifying for the play-offs, in which they were eliminated in the semi-final by Morecambe.

York entered the 2006–07 FA Cup in the fourth qualifying round, beating Newcastle Benfield away before losing at home to Bristol City in the first round. They were knocked out in the first round of the 2006–07 FA Trophy, being beaten by their eventual play-off conquerors Morecambe.

Twenty-eight players made at least one appearance in nationally organised first-team competition, and there were twelve different goalscorers. Striker Craig Farrell played in all fifty-one first-team matches over the season. Clayton Donaldson finished as leading goalscorer with twenty-six goals, of which twenty-four came in league competition, one came in the FA Cup one came in the FA Trophy. The winner of the Clubman of the Year award was Neal Bishop.

New home and away kits were brought in for the first time in two years. The home kit included red shirts with a white collar, bar a section under the neck which was red, and white trims on the sleeves, white shorts and red socks. The away kit comprised yellow shirts with a with a green collar, bar a section under the neck which was yellow, and white trims on the sleeves, blue shorts and blue socks. CLP Industries continued as shirt sponsors for the second successive season.

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