Lily was born c. 1468 at Odiham, Hampshire and he entered the university of Oxford in 1486. After graduating in arts he went on a pilgrimage to Jerusalem. On his return journey he put in at Rhodes, which was still occupied by the knights of St John, under whose protection many Greeks had taken refuge after the capture of Constantinople by the Turks. He then went on to Italy, where he attended the lectures of Angelus Sabinus, Sulpitius Verulanus and Pomponius Laetus at Rome, and of Egnatius at Venice.
After his return he settled in London—where he became friends with Thomas More—as a private teacher of grammar, and is believed to have been the first who taught Greek in that city. In 1510 John Colet, dean of St Paul's, who was then founding the school which afterwards became famous, appointed Lily the first high master in 1512. Colet's correspondence with Erasmus shows he first offered the position to the Dutchman, who refused it, before considering Lily. Ward and Waller ranked Lily "with Grocyn and Linacre as one of the most erudite students of Greek that England possessed". Lily's pupils included William Paget, John Leland, Antony Denny, Thomas Wriothesley and Edward North, 1st Baron North. The school became a paragon of classical scholarship.
He died of the plague in London on 25 February 1522 and was buried in the north churchyard of St. Paul's Cathedral.
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