He was born on November 29, 1777, in London, England.

He was an English librarian and antiquarian. Ellis was educated at the Mercers' School, Merchant Taylors' School, and St. John’s College, Oxford (B.C.L., 1802). While an undergraduate, he was initiated into library work through an appointment as an assistant at the Bodleian (1798). In 1800, he transferred to the British Museum, where in 1805, he became Keeper of printed books, and in 1812, Keeper of manuscripts. Under his direction, an organized catalogue of the British Museum library was produced in 1819. Ellis also used the resources of the Museum to produce several editions and studies of early texts, including an edition of Dugdale's Monasticon Anglicanum. He was named principal librarian of the British Museum in 1827 but proved a poor administrator, with the result that a Parliamentary commission (1835-1836) reorganized the Museum to give effective administrative control to the Secretary, Anthony Panizzi. He shared the secretary position at the Society of Antiquaries from 1848 with John Yonge Akerman, who took over in 1853. He was director of the Society from 1853 to 1857. Ellis retired in 1856.

In 1805, he married Lady Francis Jane Frost (1781–1866). He died on January 15, 1869, in London, England.