Despite financial difficulties and some doubts about her ability to complete the degree, Ellis passed her first-year examinations and returned home to Utah. She returned for her second year, pregnant and without money. By taking sewing jobs and guarding the hall of cadavers at night she earned enough to cover her tuition and living expenses. Her sixth child, a daughter, was born in the spring of her second year in Philadelphia, and mother and child did not return to Utah until after her third year, when she graduated with high honors and a Doctor of Medicine degree.

Back home in Utah, Ellis established her own practice and during her career delivered more than 5,000 children. The School of Nursing and Obstetrics, which she founded in 1879, trained five hundred women who became licensed midwives. She continued her study of medicine with graduate courses at the University of Michigan Medical School in 1893. Her medical career lasted more than fifty years and she continued to teach obstetrics classes into her eighties.