Fyvie signed for Wigan Athletic in July 2012, with the "Latics" paying Aberdeen an undisclosed transfer fee believed to be around £500,000. Wigan manager Roberto Martínez praised him for the impact he had already made during his career at Aberdeen. The midfielder agreed a three-year contract with Wigan. On 28 August 2012, he made his debut as a substitute in the League Cup against Nottingham Forest which Wigan won 4–1. Fyvie was also brought on in the following League Cup match at West Ham on 25 September which again ended 4–1 in Wigan's favour. On 30 October, he made his full debut in Wigan's starting line-up, again in the League Cup, in a surprise defeat to Bradford following a penalty shoot-out. In November and December 2012, Fyvie was part of Wigan's Premier League match day squad seven times but did not feature. In January 2013, Fyvie started in Wigan's third round FA Cup matches against Bournemouth. He was an unused substitute as Wigan won the 2013 FA Cup Final.