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Alan Percy was the second Master of the College. He was Prebendary of Dunnington in York Cathedral to which he was admitted 1 May 1513. He was admitted Master of St John's 29 July 1516, at the formal opening of the College, though he seems to have been perfoming the duties for about a month before that date. He vacated his Prebend at York in 1517 and Robert Shorton, his predecessor as Master of St John's, succeeded him there, 1 November 1517.
Percy had been appointed Rector of St Anne with St Agnes in the City of London by the Abbot and Convent of Westminster, and was instituted 6 May 1515. He resigned both his Rectory and his Mastership in 1518. The pension assigned to him by the College (£10/year) was a liberal one at the time, for the stipend of the Master was only £12. However, Percy did not claim the pension long as King Henry VIII in 1520 gave him an estate in Middlesex, whereupon, he surrendered his claim upon College revenues.