Nepean was one of thirteen children. His elder brother, Augustus Adolphus Nepean was also a cricketer with Middlesex as was his nephew, Evan Alcock Nepean. Nepean's brother, Evan Colville Nepean, father of Evan Alcock Nepean, had several children, including a daughter, Emily Margaret. She married Felton George Randolph; their daughter, Margaret Isabel married James Cassilis MacLean and in turn had a daughter, Fynvola Susan. Fynvola married James Murray Grant in 1957; their children included Hugh Grant, the actor. ' Charles Nepean died unmarried in 1903.
Sporting career
Cricket
On his arrival at Oxford, Nepean had a good reputation as a batsman. He made his debut for the University against M.C.C. on 26 May 1870, scoring 11 and 8 in a match won by the M.C.C. by 6 wickets. His next first-class match came at the end of June against Surrey, when he played as the wicket-keeper, claiming three wickets, including those of Surrey's top-scorers, Leonard Howell and Richard Humphrey; the University won the match by 3 wickets. According to his obituary in Wisden, "his future at Oxford seemed assured, but from some cause he did not get a place in the eleven till his last year"; he was described as "an admirable batsman, with a very neat and business-like style". His next first-class appearance came in May 1873 against M.C.C. In the summer of 1873, he played regularly including the two wicket victory over Middlesex in June and the match against Cambridge University at Lords, scoring 22 and 50, helping Cuthbert Ottaway to gain a victory by three wickets and for Nepean to obtain his blue. On the strength of his performances for Oxford he was selected for the Gentlemen in the first Gentlemen v Players match to be played at the Prince's Cricket Ground, in Chelsea. The Gentleman won the match by an innings and 54 runs, with A. N. Hornby and W.G. Grace scoring 104 and 70 respectively, and Grace and his brother Fred claiming 11 wickets between them. This match came between Nepean's two appearances for Middlesex against M.C.C. in June 1873 and against his former university in June 1874. Both matches ended in defeats for the county side. Following his ordination, he no longer played first-class cricket, although he was a member of the Kent committee, thus keeping him in touch with the game.
Football
At Oxford, Nepean also played football, winning a blue. In November 1870, he was selected by Arthur Kinnaird to represent "Scotland" in the second pseudo-international match against the English side, organised by Charles Alcock. The Scottish XI was made up from players from London and the Home Counties with "Scottish connections". According to the report on the match played at the Kennington Oval on 19 November 1870, "proceedings were commenced with a kick-off by C.E.B. Nepean on behalf of the Scottish team". The English won the match with a single goal from R.S.F. Walker; for the "Scotch", "C.E.B. Nepean... was a perfect rock in the way of defence".
Nepean retained his place in the Scottish team for the next three games, playing in various positions. In the match on 25 February 1871, Nepean scored the Scottish goal in a 1–1 draw; the match report says "about a quarter of an hour after the kick-off a loud shout proclaimed the fall of the English goal – an achievement entirely due to the play of C.E. Nepean". With England equalising through R.S.F. Walker, the match ended "leaving the question of supremacy undecided". The report comments: "to C. E. Nepean, Q. Hogg and W. H. Gladstone was mainly due the successful defence of lines against a series of well-organised attacks". In the last of the pseudo-internationals, played on 24 February1872, Nepean played in goal for part of the game, alternating with M. J. Muir Mackenzie; this match ended in a 1–0 victory for the English, with a goal from J. C. Clegg. In 1872, Oxford University entered a team in the FA Cupfor the first time, reaching the final against the Wanderers. Nepean had become the university's first-choice goalkeeper but was unavailable for the final, which was won 2–0 by the Wanderers. The university reached the final again in 1874; this time Nepean was available to play in goal. In the match against the Royal Engineers, Nepean repeatedly thwarted the Engineers' attempts on goal. Oxford won the match 2–0 and secured the cup. He was also a member of the Wanderers club.
Later career
On leaving Oxford in 1874, Nepean entered the Church of England and in 1876 he was appointed as vicar of Lenham in Kent. In 1894, he was appointed as vice-chairman at the inaugural meeting of Lenham Parish Council. He died on 26 March 1903 at Lenham, aged 52 years and 49 days.