He was educated at the King's School, Canterbury (about 1581) and then at Corpus Christi College, Cambridge, (1586; BA 1590; MA 1593) and Clare College, Cambridge (BD 1600). In 1597 Boys was presented to the rectory of Betshanger in Kent and to the mastership of Eastbridge Hospital in Canterbury. He also received the living of Tilmanstone in Kent in 1599 and in 1603 the rectory of Hollingbourne. In 1604 he married Angela Bargrave of Bridge, sister of the future Dean Isaac Bargrave. He resigned the vicarage at Tilmanstone in 1618 and accepted the rectory of Great Mongeham. In 1619 he was appointed to the deanery at Canterbury under the patronage of Archbishop George Abbot.
He is recorded as having a notable library. The engraved title page of his Works show him in his study surrounded by books; the monument on his tomb in the Lady Chapel at Canterbury has pillars carved as piles of books.
The following book from his library may have come to the Chapter Library through a bequest by Archbishop Abbot.
- Shelfmark W/H-2-28/29
- Henry Ainsworth. Annotations upon the five bookes of Moses, and the Booke of the Psalmes. Wherein the Hebrew words ... are compared and explained by the ... Greeke and Chaldee versions, ... By H.A.
- Inscription on front free endpaper of vol. 2: Jo: Boys Feb. 27. 1623.
- History of Canterbury Cathedral (1995) plates 31 and 138.