Baumgardner grew up in Fargo, North Dakota and attended Lawrence University in Appleton, Wisconsin, graduating in 1992. Subsequently, she moved to New York City where she took a job writing for Ms. Magazine.
She lives in Brooklyn with her son Skuli. Baumgardner wrote a book about bisexuality after having a long term relationship with Amy Ray of the Indigo Girls.
She has since written for numerous magazines, including Glamour, The Nation, Babble, and Maxim. Her books include Manifesta: Young Women, Feminism and the Future, Grassroots: A Field Guide for Feminist Activism written with Amy Richards, and Look Both Ways: Bisexual Politics. She produced the documentary film Speak Out: I Had an Abortion, which tells the story of ten women's abortion experiences from the 1920s to the present. She has written about purity balls (rituals celebrating virginity), about Catholic hospitals taking over secular ones and eliminating their reproductive services, and about breastfeeding her friend's son.