Sir John Ellys or Ellis (1634?–1716) was an English academic, Master of Gonville and Caius College, Cambridge from 1703.
He was born at Huntingfield, into a well-known East Anglian family; the Ellyses of Great Yarmouth, his relations, are mentioned for example in the Journal of Rowland Davies, and Anthony Ellys was a great-nephew, son of Anthony Ellys who was mayor there. His father was John Ellis or Ellys, of Raveningham or Frostenden, with two brothers, Anthony and Thomas.The Perlustration of Great Yarmouth by Charles John Palmer gives his mother as Mary Barre of Syleham.
After studying in a number of Suffolk schools, Ellys matriculated at Caius in 1648, aged 14. He graduated B.A. in 1652, and M.A. in 1655. He was then a Fellow of Caius from 1659 and in 1703 (N.S.) became Master, succeeding James Halman, who had died.
Ellys was a personal friend of Isaac Newton. He helped Newton with astronomical observations, and was one of the few who knew Newton at Cambridge who visited his rooms.
Ellys was also noted as a leading tutor across the university, popular and distinguished; and was not ordained, but held the degree of M.D. A tutorial pupil, Henry Wharton, was taught by Newton, and is thought to have been the only undergraduate student to have seen Newton's mathematical papers. Another tutorial pupil was Samuel Clarke, and Ellys had him translate the Traité of Jacques Rohault (from French to Latin, creating a textbook). It has been argued that Ellys was introducing his pupils to Newtonian thought by the 1690s.William Whiston also claimed credit for the Newtonian edge to Clarke's Rohault translation (which however went to several editions); and Richard Laughton was thought by W. W. Rouse Ball to have been another Newtonian influence on Clarke. Ellys, however, is now considered a more likely source.