The new foundation of St. John's College, Cambridge, chose him as their second master on 29 July 1516, probably with an eye to his Lancastrian connections and family influence, But he resigned the mastership two years later on 1 November 1518; the college granted him a small pension and some residence privileges.
In 1526 Thomas Boleyn, Viscount Rochford presented him to the rectory of Mulbarton, Norfolk.
He became Master of the collegiate church of the Holy Trinity at Arundel, where he succeeded the musician Edward Hygons at some point between 1535 and 1539.
But an eventual dissolution of the college was prompted at court by Henry Lord Maltravers; and a late stage Percy joined with the two fellows in surrendering it to the king on 12 December 1545.
[2] Percy died in May 1560, and was buried in the old chapel of St. John's College, where there were a brass and a marble tomb to his memory.