Maloney, who turns 30 next Thursday, has signed until the summer of 2015 by which time he will be 32.
The move has been taken following the impressive form of the former Celtic forward since his integration into the Latics first team last season.
Maloney has grown to be a firm fans' favourite at the DW Stadium and Roberto Martinez is delighted with the news.
Speaking to the club's official website, he said: “We’re delighted that Shaun has committed his future to the club. From the first day he arrived his professionalism and determination to succeed has been outstanding and an example for the younger members of the group to follow.“Shaun is one of the most technically gifted British players that you will find, but on top of his style and footballing flair his work-rate and purpose in his performances make him a key member of our future at Wigan Athletic. “I’m sure the fans are looking forward to watching him continue to enjoy his football at Latics for a long time.” Maloney was intrumental in the fight for survival last season and of course scored thehistoric goal in our first ever victory over Manchester United.