In 1895, Woolley began teaching biblical history and literature at Wellesley College. She was popular among her students and peers and, in 1896, she was made an associate professor. By 1899, she had been promoted to full professor. During her time at Wellesley, she made significant changes in the curriculum while gaining administrative experiences as the chair of her department. She also met Jeannette Augustus Marks, a student at Wellesley. Beginning in 1899, the two women lived in a life-partnership for 48 years.