The National League North club - FA Trophy winners last season - are sitting fourth after falling just short in their promotion quest last season.
Wilkin has been at the helm since 2015 and will take his time at the club to six years with this new deal.
Managing director Janene Butters says the club had no hesitation in offering new terms
“We are delighted that Kevin has committed his future to Brackley Town,” said the club’s MD.
“The club has a strong vision to build on recent successes and Kevin has an important part to play in this.
“We recently announced exciting plans for the further development of our St James Park stadium and Kevin has the backing from the club’s directors to pursue further success on the pitch.
“The club’s victory at Wembley in 2018 and place in the National League North play-off final were unprecedented and put Brackley Town on the map.
“Under Kevin Wilkin we look forward to continued success.”