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 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.
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.
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.
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.
In 1711 he was deprived of it by Robert Harley, and he petitioned to be reinstated at the accession of George I. Ellis sat for Harwich, Essex, in the parliaments of 1702–5 and 1705–8, and in 1710 unsuccessfully contested Rye, Sussex.
In 1872 the trustees of the British Museum purchased from Thomas Parker, 6th Earl of Macclesfield a voluminous collection of Ellis's official and private correspondence and papers extending from 1643 to 1720.
His intrigue is mysteriously alluded to in six lines of Alexander Pope's Sober Advice from Horace, implying that, having offended the duchess by boasting of the intimacy, he was, at her instigation, castrated.