 In 1494 he resigned his benefice to become proctor of the university and three years later was appointed master debater, about which date he also became chaplain and confessor to Margaret Beaufort, Countess of Richmond and Derby, mother of King Henry VII.On 5 July 1501, he became a doctor of sacred theology and 10 days later was elected Vice-Chancellor of the University.Under Fisher's guidance, his patroness Lady Margaret founded St John's and Christ's Colleges at Cambridge, and a "Lady Margaret Professorship of Divinity" at each of the two universities at Oxford and Cambridge, Fisher himself becoming the first occupant of the Cambridge chair.