The 23-year-old, who made his full debut for the Championship side in December, will now remain at the DW Stadium until the summer of 2017.
Wigan manager Uwe Rosler has said that he is delighted to see Kiernan commit his future to the club.
"It is fantastic when a young player can progress through the ranks of a club," he told Wigan's official website.
"He earned his chance with us and was very consistent when he came into the team. His performances were a major positive in the second half of the season.
"I am delighted to be able to keep working with him now, exactly the kind of player we want to bring into the squad and become part of the backbone of the team in the future."
Kiernan has made 14 appearances for Wigan.