After Crystal Palace failed to gain promotion, Boyce returned to Premier League football in 2006, this time with Wigan Athletic after completing a move for a fee of £1 million, and was a key player during his first season when the club narrowly avoided relegation. He remained an active member of the first-team throughout his spell at Wigan, and is the club's Premier League appearance record holder. In May 2013, he captained Wigan Athletic to victory in the 2013 FA Cup Final in a 1–0 win over Manchester City. He last played for Blackpool in the 2015–16 League One season.