Woomes Chunder Bonnerjee was the son of Girish Chunder Bonnerjee, an attorney, and his wife, Saraswati Devi. He was educated at the Oriental Seminary and the Hindu School, Calcutta. Concerned at his negligence, his father removed him from school and in 1861 articled him to a local British solicitor. Bonnerjee won a government scholarship to study Law in England in 1864 and lodged at 108 Denbigh Street, St George's Road, London. He was admitted a student of  Middle Temple on 19 November 1864 and was called to the Bar on 11 June 1867. He was a founder and Secretary of the London Indian Society, and advocated representative and responsible government in India. He then became a member of the East India Association, which superseded the London Indian Society.

Bonnerjee left England in 1868, and on 12 November was enrolled as an advocate at the Calcutta High Court. He became involved with Calcutta University; he was a member of its syndicate, President of its Faculty of Law (1884), and its first representative on the Legislative Council (1894–5). Bonnerjee was one of the founder-members of the Indian National Congress in December 1885. Proposed by Allan Octavian Hume, he was unanimously elected the first President. In the meantime, Bonnerjee travelled between India and Britain: he sent his four-year old son Shelley, and young Nolini and Susie to be educated in Britain in 1874. He and his wife, Hemangini, travelled to and fro, bringing their children to be educated in Britain. In 1888 Hemangini settled permanently in London.

Wealthy from the Bar, Bonnerjee, in about 1890, bought a large house, 8 Bedford Park, Croydon, Surrey, which he named Kidderpore. Bonnerjee lived partly in England and partly in India until 1902, thereafter living mostly at Croydon and practising before the Judicial Committee of the Privy Council. He died at his home, Kidderpore, on 21 July 1906. Although Hemangini had converted to Christianity, W. C. Bonnerjee had remained a Hindu, but was given a non-religious burial in England, as according to his wishes. Hemangini returned to India after his death and died in 1910. Their descendents live in India and Britain.