The Applause singer, who graces the US magazine's cover this month, was one of several women celebrated at the annual event at New York City's Carnegie Hall.
Gaga, real name Stefani Germanotta, was recognised with the Monster Talent Award for her Born This Way Foundation, founded by the star and her mother in 2011 to "empower youth and inspire bravery".
Editor-in-chief Cindi Leive saluted the star, and others, for making a difference.
"Glamour's Women of the Year awards are all about saluting women whose work helps to change the world, and that mission has clearly been accomplished with this year's group of honourees. I'm so blown away by the range of achievement, bravery, depth, smarts, and moxie they have demonstrated," she said.
Lily presented the Game Changer award to Hawaiian surfer Carissa Moore, credited with raising the profile of women in the sport.
Lena meanwhile honoured Melinda Gates with the Advocate award for her work in global health.
Comedian Seth Meyers hosted this year's ceremony, which supported The Malala Fund, an organisation fighting for the right to education for girls and women around the globe.