Ellis belonged to a family "of great antiquity and good account", and finished his theological studies at the English College at Douay. On 25 August 1628 he was sent from Douay, with nine other students, under the care of the Rev. Joseph Harvey, to take possession of the newly founded English College of Lisbon. There he pursued his theological studies under Thomas White (alias Blackloe), and by degrees became professor of philosophy and divinity, doctor in the latter faculty, and president of the college. Afterwards he returned to England, and was elected dean of the chapter[which?] at the general assembly held in November 1657, but he did not take the oath attached to the office until 14 October 1660, although in the meantime he acted in the capacity of dean.
By his brethren of the chapter he was highly esteemed, but his position naturally rendered him obnoxious to the Jesuits and Franciscans, who were strongly opposed to the introduction of a bishop. The Abbot Claudius Agretti, canon of Bruges and minister apostolic in Belgium, who was sent by Pope Clement IX on a special mission to examine into the condition of ecclesiastical affairs in England in 1669, stated in his report that Ellis was extremely anxious for the confirmation of the chapter, and was even willing that his holiness should create a new dean and chapter, omitting all the existing members. Agretti doubted, however, whether they would really assent to this sacrifice. He described Ellis as 'noble, esteemed, learned, and moderate, but withal tinged with Blackloeism.' Ellis died in July 1676.