In 1798, through his friend
John Price, Ellis was appointed one of the two assistants in the
Bodleian Library, the other being his future colleague in the British Museum
Henry Hervey Baber. He took the degree of B.C.L. in 1802. He was a Fellow of St John's till 1805. In 1800 he was appointed a temporary assistant in the library of the British Museum, and in 1805 he became assistant-keeper of printed books under
William Beloe. The theft of prints which cost Beloe his appointment in the following year raised Ellis to the headship of the department, and Baber became his assistant. In 1827
Joseph Planta, the principal librarian, died, and Ellis, who had for nine years taken on much of his duties, expected to succeed him. When two names for the vacancy were submitted to the Crown,
Henry Fynes Clinton, a protégé of Archbishop
Charles Manners-Sutton, was placed before Ellis. Ellis intrigued successfully for the post, it is said by pursuing the carriage of the royal physician,
Sir William Knighton, and enlisting his good offices with the king. He was appointed on 20 December 1827. In 1832 he was made a
Knight of Hanover, an honour which he shared with
John Herschel,
Frederic Madden, and others; and he was knighted in 1833. ==In the face of reform==