Good form last season saw him earn his first cap for Scotland as he came on as a substitute in the 1-1 draw with Moldova.
In 149 league games, Lee has scored 24 goals for the Latics, and he has had 8 in 26 games for the team this season.
Rotherham away in just under two weeks will be his 150th league game for the club.
He told the clubs official site: "I'm delighted to commit my future to the club and it's really pleasing to have got everything sorted out. I've loved my time here and to be honest I didn't want to think about going anywhere else. I'm a different player to the one that joined the club but I am enjoying my football and therefore had no doubts about signing a new deal once it was agreed.
"We have made great progress as a club since I have been here and hopefully we can go one step further come the end of this season. It has always been my ambition to play in the Premiership and hopefully that will happen with Wigan Athletic. There is a long way to go but we are in a decent position to push on and that's what we must try and do.
"Though I still regard myself as a striker, I was never the most prolific and therefore in some ways I suppose I may be more suited to the midfield role. It's a tough one to play but I think I have adapted to it quite well and I certainly enjoy it out there. It's hard work defensively but it does still allow me the freedom to get into the box and go for goal and that is something I enjoy. I've got eight goals for the season so far which isn't too bad and hopefully I can build on that and move into double figures. The most important thing though is that the team does well and hopefully I can continue to play my part in the growth of this club.
"As I said, I'm delighted to have agreed a new deal and I look forward to the years ahead. This contract extension gives me security for my future and that means that all I have to worry about and focus on now is my football. With the crucial part of the season now ahead of us, that is exactly what I am intending to do."