Charles Gordon O'Neill was born in Glasgow, Scotland, probably in 1827 or 1828, the son of Mary Gallagher and her husband, John O'Neill, a hotel proprietor. He studied civil engineering and mechanics at the University of Glasgow and then served for 14 years as assistant superintendent of the city's public works.
O'Neill emigrated to New Zealand, arriving in Otago on 24 January 1864. That year he was appointed district engineer for the southern district and surveyor for the Otago provincial government. From 1864 to 1866 he laid out the town of Milton. He moved to the Thames district in 1868 where he was appointed a mining surveyor for the Thames goldfield and engineer-in-chief of railways, tramways and wharves. He designed the goldfields' tramline. In 1869 he was appointed provincial engineer and chief surveyor of the goldfield and the same year was made a justice of the peace. In 1871 he surveyed and reported on a proposed railway route across the Remutaka Range. In 1874 he was a member of a royal commission which inquired into a boiler explosion at the Kurunui battery on the Thames goldfield in which three people were killed.
From 1866 to 1870 O'Neill was MHR for Goldfields, Otago, and from 1871 to 1875 represented Thames. His main legislative concerns were the provision of reserves, the widening and regulation of streets, and that all plans of towns should be approved by the governor before land went up for sale. A bill he put forward was rejected on the Speaker's casting vote, but the Plans of Towns Regulation Act 1875 incorporated his main proposals.
Charles O'Neill took up residence in Wellington in 1876. In August 1878, together with Thomas Kennedy Macdonald and John Henderson, he opened the first steam street-rail tramway system in the southern hemisphere. It consisted of six engines and 14 passenger cars running from the railway station at Pipitea Point on Thorndon Quay to the Basin Reserve and Adelaide Road. A branch line extended from Lambton Quay to the wharf. After two years' operation the steam tramways were found to be too expensive. Moreover, horses were frightened by the trams and, on one occasion, cabbies protested against the tramway by lining the route three deep. In 1880 the entire system and rolling stock were sold and converted to horse traction, although the steam engines were used for many years on the Sanson–Foxton railway.
O'Neill also practised as an architect. He designed the keeper's residence, coach-house and stables at the Kaiwharawhara powder magazine. In 1879 he took samples of New Zealand flagstones to Australia in an attempt to attract capital for starting a New Zealand industry. Although unsuccessful, he won a prize for his flagstones at the 1879 Sydney International Exhibition.
Before he came to New Zealand O'Neill had been active in the Society of St Vincent de Paul, set up to help the poor, and he continued this work to the end of his life. He was president of its Wellington conference and promoted the society in Australia, where he lived from 1881. Ironically, owing to the collapse of the Northumberland Banking Company, of which he was a director, he himself became financially embarrassed. O'Neill died in St Vincent's Hospital in Sydney on 8 November 1900. He had never married.