Born in Chester, Cheshire, Heaton began his football career with Wrexham, for whom he played both in goal and in midfield, but, after making 20 appearances for the Manchester United Under-17 team in the previous two seasons, he signed for United as a trainee on 8 July 2002. He became a regular in the Under-17 team during the 2002–03 season, and picked up an FA Youth Cup winner's medal despite playing second fiddle to Luke Steele throughout the entire competition. He made his first appearance in the reserve team the following season, starting in a 3–1 home win over Birmingham City in the Premier Reserve League on 2 October 2003. At the end of the 2003–04 season, Heaton was named on the bench for the final of the Manchester Senior Cup against Manchester City, and won a winner's medal despite not taking the field.