The tight-head prop made his Warriors debut in 2015 and has gone on to play 72 times for the club and has 18 caps for his country. His new deal will keep him at Glasgow until at least 2022.
Fagerson, 22, is a product of the High School of Dundee and Strathallan and after coming through the Scottish Rugby Academy system signed his first professional contract with the Warriors in March 2015.
Fagerson was in excellent form early this season before getting injured in Glasgow's victory over the Toyota Cheetahs in Bloemfontein. He is exected to return to full fitness early in the new year.
He becomes the 10th player to commit his future to the Warriors over the last couple of weeks.
Speaking to glasgowwarriors.org, Fagerson said: "I'm so happy to be staying at Glasgow Warriors. The club means a lot to me, so to be able to stay for at least another three years is a huge honour.
"We have a world-class coaching team and a growing number of passionate supporters, so it's a great club to be at.
"I love playing at Scotstoun and I believe I can achieve everything I want to achieve in the game here at the Warriors."
Glasgow Warriors Head Coach, Dave Rennie, added: "Zander's a good man and a terrific prop. He is physical and mobile and at only 22 I believe he'll continue to develop in our environment. We're thrilled that he has committed his long-term future to the club.
"It's great that we've been able to secure a large number of players on new contracts over the last couple of weeks and that our players want to stay in Glasgow and play for this club."