Morton was born in Plymouth, Massachusetts, the daughter of Edwin Morton and Betsy Torrey Harlow Morton. Both of her parents were also born in Plymouth. She was descended from Puritan leader George Morton, and through that connection was related to many prominent New Englanders. She attended Antioch College and the Woman's Medical College of Pennsylvania, then completed her medical degree at the New England Female Medical College in 1862. She had further training in obstetrics in Paris."Dr. Helen Morton" Woman's Medical Journal 28(11)(November 1918): 238-239.
