Eliot was born at the village of Sibford Gower near Banbury, Oxfordshire, England and educated at Cheltenham College and Balliol College, Oxford, where he took a double first in classical moderations and Greats, as well as winning the Craven, Ireland and Hertford scholarships. Remarkably, he also won the Boden Sanskrit Scholarship and the Houghton Syriac prize. A brilliant linguist, Eliot served in diplomatic posts in Russia (1885), Morocco (1892), Turkey (1893), and Washington, D.C. (1899). In 1900, he was knighted and also became commissioner of British East Africa.
In April 1902, the first application for land in British East Africa was made by the East Africa Syndicate - a company in which financiers belonging to the British South Africa Company were interested - which sought a grant of 500 sq. m., and this was followed by other applications for considerable areas, a scheme being also propounded for a large Jewish settlement. During 1903 the arrival of hundreds of prospective settlers, chiefly from South Africa, led to the decision to entertain no more applications for large areas of land, especially as questions were raised concerning the preservation for the Masai of their rights of pasturage. In April 1903, Major Frederick Russell Burnham, the famous American scout and then a Director of the East African Syndicate, sent an expedition conisting of John Weston Brooke, John Charles Blick, Mr. Bittlebank, and Mr. Brown, to assess the mineral wealth of the region. The party, known as the "Four B.'s", traveled from Nairobi via Mount Elgon northwards to the western shores of Lake Rudolph, experiencing plenty of privations from want of water, and of the danger from encounters with the Masai.
In the carrying out of this policy of colonization a dispute arose between Eliot and Lord Lansdowne, the British Foreign Secretary. Lansdowne, believing himself bound by pledges given to the East Africa Syndicate, decided that they should be granted the lease of the 500 sq. m. they had applied for; but after consulting officials of the protectorate then in London, he refused Eliot permission to conclude leases for 50 sq. m. each to two applicants from South Africa. Eliot thereupon resigned his post, and in a public telegram to the prime minister, dated Mombasa, the 21st of June 1904, gave as his reason:- "Lord Lansdowne ordered me to refuse grants of land to certain. private persons while giving a monopoly of land on unduly advantageous terms to the East Africa Syndicate. I have refused to execute these instructions, which I consider unjust. and impolitic." On the day Sir Charles sent this telegram the appointment of Sir Donald William Stewart, the chief commissioner of Ashanti (Ghana), to succeed him was announced.
After his service in British East Africa he was Vice-Chancellor of the University of Sheffield until 1912 when he was appointed the first Vice-Chancellor of the University of Hong Kong in Hong Kong from 1912 to 1918.
A lifelong bachelor, Eliot died at sea in the Straits of Malacca.