The new three-and-a-half year deal will keep the 22-year-old at the DW Stadium until the summer of 2017.
Wigan boss Owen Coyle told the club's website: "It's great news, and a sign of our intent to secure the long term future of Wigan Athletic.
"We want to keep hold of our best young talents, and Callum certainly represents that.
"He is an integral part of our plans now, and what we want to build at the club moving forwards with players like Callum a key part of that."
McManaman added: "I'm delighted to get my future sorted. This is where I made my debut and got my break in football and I just want to thank the Manager for having faith in me.
"A big thanks to the Wigan fans as well, for their support in every game, it makes a big difference to me and makes my family so proud. It means so much.
"Now I just need to get my head down, keep working hard and hopefully keep my place in the team and do everything I can to help the team be successful."