The Latics have rewarded the 51-year-old with an extended deal for guiding them to the League One title and the quarter-finals of the FA Cup this season.
"I have loved every minute of my time here. It has been a huge team effort and I couldn't have achieved anything here without the support of our chairman David Sharpe, chief executive Jonathan Jackson, my coaching staff, all the staff across the club and the players," Sky Sports News quotes Cook as saying.
"It was always going to be a big challenge to win promotion immediately but a lot of hard work and endeavour has gone in from so many people, who can all look back on the past year with great pride.
"Our supporters have been incredible, from the first day I arrived I couldn't have been more welcome and I look forward to seeing everyone back at the DW next season."
Wigan sealed the league title over the weekend when they defeated Doncaster Rovers.