He was elected Master (head) of Balliol College, Oxford on 2 September 1559, a post he held until he resigned the following year on 27 October 1560.
In 1557 and 1558, he successively took his Bachelor's and Doctor's degrees in Divinity; but Wood adds a special warning that such rapid promotion was only because Oxford University was very empty, and wanted "theologists to perform the requisite offices."
It is only fair, however, to add that in another passage Wood mentions Francis Babington as renowned for his philosophical and logical disputations.
In 1559, Queen Elizabeth I's visitors removed William Wright from the mastership of Balliol College, Oxford, and appointed Dr Babington instead.
Anthony à Wood tells us that he was one of Leicester's five most trusted advisers in Oxford, and was chosen to preach Amy Robsart's funeral sermon at St Mary's Church, Oxford, on which occasion he "tript once or twice by recommending to his auditors the virtues of that lady so pitifully murdered instead of so pitifully slain."
Strype, in his account of this contest, describes Dr Babington as "a man of mean learning and of a complying temper",[10] but he failed in his candidature.