Helen Magill was born in Providence, Rhode Island, to Edward Hicks Magill and Sarah Warner Beans. She was the eldest of six children in a Quaker family. Magill was brought up to believe that she deserved the same education as a man and all five Magill daughters were educated to become college teachers. In 1859, the family moved to Boston, Massachusetts, where Magill enrolled as the only female student in the Boston Public Latin School. Her father taught French and Latin there for three years, and he was promoted to submaster.