Hunt was born in Chicago, Illinois, to Robert Edward Hunt, an electrician, and Alice E. Hunt (née Jatczak). Her father was of Irish and Belgian ancestry and her mother is of Polish descent. She has three older brothers named Patrick, Kevin, and Tom, two older sisters named Cathy and Carol, and a younger sister named Mary. She was educated in Catholic schools, attending St. Ferdinand Grammar School and Notre Dame High School for Girls in Chicago, and worked part-time as a nurse's aide.
In 1982, Hunt worked as an oncology nurse at Northwestern Memorial Hospital in Chicago. In 1984, she co-founded an improvisational comedy troupe called An Impulsive Thing. Hunt also performed as a member of Chicago's world-famous the Second City, joining in 1986. In 1988, while a nurse, Hunt auditioned on her lunch break for the role of waitress Sally Dibbs in Rain Man and won it.
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She shares the same name as her Toy Story character Dolly's owner Bonnie Anderson, as well as her own other role Bonnie Hopps, who is instead from Zootopia.