On 1 August 2006, Boyce was signed by Wigan Athletic on a four-year deal for an initial fee of £1 million. He was initially signed as a replacement on the right side of defence for Pascal Chimbonda, but was often deployed as a centre back. He made his debut for the club on 19 August 2006 in a Premier League match against Newcastle United. He made 34 league appearances during the season, helping the club avoid relegation, which was confirmed on the final day of the season in a 2–1 win against Sheffield United. His performances earned him praise from Wigan supporters, and he narrowly missed out on the club's Player of the Year award.