He was elected to a studentship at Christ Church, Oxford, in 1665, and proceeded Bachelor of Arts (BA) 19 June 1669.
In 1676 he was appointed, along with his brother Welbore Ellis, customer, comptroller and searcher for the Irish provinces of Leinster and Munster; and while holding this sinecure acquired considerable property in Ireland.
He acted as secretary to Richard Talbot, 1st Earl of Tyrconnell, on the latter's appointment to the lord-lieutenancy of Ireland in 1687, and was knighted.
Accompanying James II to Ireland he was placed on his privy council and appointed one of the assessors of Dublin in April 1690.
He was attainted in 1691, and his older brother John Ellis, to whom he owed money, gained possession of his Irish property.