Fortier has coached at Gonzaga for seven seasons, including the Bulldogs' current run of six consecutive trips to the NCAA tournament.
Terms of her contract were not disclosed.
Fortier inherits a team that went 29-5 and was ranked in the Top 25 most of last season.
The Bulldogs won the West Coast Conference for the 10th straight year and earned a bid to the NCAA tourney, where they lost to James Madison in their first game.
"I am very excited to announce Lisa Fortier as our new head women's basketball coach," athletic director Mike Roth said. "She is a tireless recruiter who will continue the tradition of bringing tremendous student-athletes to Gonzaga and then developing them into great college basketball players."
Fortier said she is grateful for the opportunity to lead a program she helped develop into a perennial Top 25 team.
"I'm truly excited to continue working with the talented group of young women we currently have in our program," Fortier said.
In her seven years as a Gonzaga assistant, the Bulldogs have produced an overall record of 196-43. They have gone 98-8 in the WCC.
Fortier served as the coordinator of basketball operations at Gonzaga from 2004-06, then left for a season to work as an assistant at Northern Colorado.
Since returning to Gonzaga, Fortier has worked as the defensive coordinator, recruiting coordinator and coach of the guards. The Bulldogs were one of the best defensive squads in the nation this season, allowing just 56.5 points per game.
Fortier has coached two WNBA draft picks in Courtney Vandersloot and Katelan Redmon.
A native of Grass Valley, Calif., Fortier played college basketball at Cal State-Monterey Bay and Butte (Calif.) Community College.
She graduated from Monterey Bay in 2004 with a bachelor's degree in human communications, and later earned a master's in sport and athletic administration from Gonzaga.