The 2012–13 season was Bolton Wanderers first season in the Football League Championship since 2001 following their relegation from the Premier League. Bolton ultimately missed out on a play-off spot, being overtaken by Leicester City on the final day of the season, meaning Bolton spent the 2013–14 season in the Championship.

The season covered the period from 1 July 2012 to 30 June 2013.

On 24 May, Bolton announced an initial ten fixtures to precede the 2012–13 season. These took in away games at League One sides Crewe Alexandra, Portsmouth, Tranmere Rovers and League Two sides Morecambe and Accrington Stanley. They also played five non league sides, Bamber Bridge, Radcliffe Borough, Chorley, Barrow and Halifax Town. All five of the latter games, along with the game at Accrington Stanley and another game at Daisy Hill which was announced on 2 August, were played by a Development squad. An additional game, the only one to be played at the Reebok Stadium, against Barcelona B, the reserve side of Barcelona, was announced on 29 June. On 6 June, a tour of Scotland was announced, with the team visiting Ayr United, Hamilton Academical and Falkirk.