The long-serving lock made his debut in 2011 and has been a regular fixture in the side since. The new deal will extend his stay into next season, his 13th with the club.
The 31-year-old has helped Edinburgh climb to the top of the United Rugby Championship this season and was also part of the side which defeated Saracens away in the European Challenge Cup.
Gilchrist has made 167 appearances for the club – the most by an Edinburgh lock – and is currently fifth on their all-time appearance list, two games shy of head coach, Mike Blair.
Gilchrist, a product of Alloa RFC, said: “I’m absolutely delighted to sign a new deal. The club means so much to me. I’ve been at Edinburgh over a decade, so to be given the opportunity to stay and continue to play my rugby here means everything.”