In January 1545, after two months in the post of master of Corpus, he was elected vice-chancellor of the university. During his year in office he got into some trouble with the Chancellor of Cambridge University, Stephen Gardiner, over a play, "Pammachius", performed by the students and censored by the college, which derided the old ecclesiastical system. Parker was obliged to make enquiries into the nature of the play, but then allowed to settle the matter himself on behalf of the university authorities.