Ellen Mahaffy originated in a small town south of Rochester, New York, known as Lima. A high school art elective led to her lifelong commitment to photography. After her high school photography teacher convinced her that going to college for art would suit her more than computer science, she made her way to Baltimore, Maryland, where she earned a BFA in photography from the Maryland Institute College of Art.
After returning to Rochester, she attained a MFA from the College at Brockport and Visual Studies Workshop. Her multimedia project, Nothing Was Ever Said, unearthed familial secrets. Her study of queer theory inspired her to produce portraits that explore sexuality.
Currently, she is an associate professor in the department of communication and journalism at the University of Wisconsin–Eau Claire, where she teaches courses in visual communication. She is also the co-founder and an executive director of the Eau Queer Film Festival (2010–present).