The Hatters boss has been handed the new deal after guiding the North West outfit to First Division safety last season.
It has nott been an easy 12 months for Kilner, however, as his position did seem to be in serious doubt when chairman Brendan Elwood invited former Liverpool boss Roy Evans to join the backroom staff.
Evans turned down the offer, however, and Kilner rode the storm, eventually leading his side to safety.
Meanwhile, Lee Jones, Mike Flynn, Aaron Wilbraham, Ali Gibb, Robert Clare and Karim Fradin have also agreed new contracts with the club.
