John Ellis (1643–1738) was an English official and Member of Parliament.
Born in or about 1643, he was the eldest son of John Ellis, author of Vindiciæ Catholicæ, by his wife Susannah, daughter of William Welbore of Cambridge. He received his education at Westminster School, and was elected student of Christ Church, Oxford, in 1664. At college he met Humphrey Prideaux, with whom he formed a lifelong friendship. Ellis did not take a degree, but obtained employment in the secretary of state's office.
In March 1672 he was under Sir Joseph Williamson in the paper office, Whitehall. On the promotion of Williamson to be secretary of state in the autumn of 1674 Ellis lost his situation. He obtained, however, the appointment of secretary to Sir Leoline Jenkins, one of the envoys chosen to attend the conference at Nijmegen, the Netherlands, and set out 20 December 1675. He was employed in this capacity until September 1677. His doings during this period of his life were set down in his Journal of Proceedings of the Nimeguen Conference, 1674–1677, and Note Book at Nimeguen, 1675–6. From 1678 to 1680 Ellis acted as secretary to Thomas Butler, 6th Earl of Ossory. At the beginning of 1680 he made another journey into the Netherlands to lay before the States-General the claims of Lord Ossory to the rank of general, which the latter had received from the Prince of Orange. He was successful in obtaining the necessary confirmation. After the death of Ossory in August 1680 Ellis became secretary to his father, James Butler, 1st Duke of Ormonde, then lord-lieutenant of Ireland. In October 1682 he received the appointment of secretary to the commissioners of the revenue of Ireland, a post he continued until the Glorious Revolution.
He left Dublin for England early in 1689, and his place at the Irish treasury was filled up by some one on the spot. Towards the end of 1689 he became secretary to James Butler, 2nd Duke of Ormonde, as he had been before to his father, the Earl of Ossory. Two years later he was one of the commissioners of transports, and finally under-secretary of state in May 1695. He filled for ten years the office of under-secretary to four successive secretaries of state; but after some misunderstanding with Sir Charles Hedges, he resigned in May 1705. William III had given him the place of comptroller of the Mint, worth £500 a year on 23 May 1701. The office was confirmed to him in the next reign by letters patent of 11 June 1702. In 1711 he was deprived of it by Robert Harley, and he petitioned to be reinstated at the accession of George I.