Conolly was born at Market Rasen, Lincolnshire, of an Irish family. He spent four years as a lieutenant in the Cambridgeshire Militia and lived for a year in France before embarking on a medical career. He graduated with an MD degree at University of Edinburgh in 1821. After practising at Lewes, Chichester and Stratford-on-Avon successively, he was appointed professor of the practice of medicine at University College, London, in 1828. In 1830 he published a work on the Indications of Insanity, and soon afterwards settled at Warwick.
In 1832 in co-operation with Sir Charles Hastings and Sir John Forbes, he founded a small medical association with a view to raising the standard of provincial practice called the Provincial Medical and Surgical Association. His brother William Brice Conolly became the association's 'Widows and Orphans Benevolent Fund' treasurer and secretary. In later years this grew in importance and membership, and finally became the British Medical Association.
Conolly and Forbes went on to start a new publication in 1836: the 'British and Foreign Medical Review, or, A Quarterly Journal of Practical Medicine', for which they shared the editorship from 1836 to 1839. It was the first publication of its type, aimed at sharing newly-won medical knowledge. The Review was read widely in Europe and America, and helped to promote modern methods of treatment and to enhance the reputation of British medicine. The BMA library still holds a complete set of its volumes.
In 1839, Conolly was appointed resident physician to the Middlesex County Asylum at Hanwell (now known as West London Mental Health NHS Trust's St Bernard's Hospital). In this capacity, he introduced the principle of non-restraint into the treatment of the insane. This principle had already been put into practice in two small English asylums—William Tuke's York Retreat and the Lincoln Asylum—but it was due to Conolly's courage in sweeping away all mechanical restraint in a great metropolitan asylum and in the face of strong opposition, that non-restraint became accepted practice throughout the country.
In 1844 Conolly ceased to be resident physician at Hanwell, but he remained visiting physician until 1852.
Conolly died on 5 March 1866 at Hanwell, where in the later part of his life he had a private asylum called Lawn House.
Conolly married Elizabeth Collins, daughter of naval captain Sir John Collins, by whom he had four children. Their only son, Edward Tennyson, was born whilst Conolly was working at Chichester in Sussex. Edward became a lawyer, having been called to the Bar on 30 January 1852. In 1865 he emigrated with his family to Picton, New Zealand. There he continued to practise law and became very active in politics. In line with his father's concerns for humane treatment of the mentally ill, he introduced the concept of rehabilitation to the New Zealand penal system. He died in Auckland in 1908 and was interred in the City of Westminster Cemetery.
John Conolly's second daughter, Sophia Jane, married Thomas Harrington Tuke in 1852. Tuke ran a private Lunatic Asylum at Manor House in Chiswick, Middlesex. (This Tuke is not related to the Tukes of the York Retreat.)
Conolly's youngest child, Ann, married Henry Maudsley when she was thirty-six, just two months before her father's death. Conolly's obituary was written by Maudsley and shocked many by its unusually unsympathetic tone. Henry Maudsley had by then taken over the running of Lawn House. Ann predeceased Maudsley on 9 February 1911 at the age of 81.
Conolly's publications include:
- Construction and Government of Lunatic Asylums (1847)
- The Indications of Insanity with an introduction by Richard Hunter and Ida MacAlpine. Psychiatric Monograph Series 4 (reprint: Dawsons, London, 1964)
- Conolly, John (1830) An Inquiry concerning the Indications of Insanity, with Suggestions for the Better Protection and Care of the Insane. John Taylor, London. - Books Google; Accessed 2007-06-06
- The Treatment of the Insane without Mechanical Restraints (1856) German translation by Caspar Max Brosius as Die Behandlung der Irren ohne mechanischen Zwang (1860)
- Essay on Hamlet (1863)
- The Transactions of The Provincial Medical and Surgical Association. 1845 Vol 1. Accessed 2007-06-17.
- Forbes, John (ed.); Conolly, John (ed.)(January - April 1836).British and Foreign Medical Review, or, A Quarterly Journal of Practical Medicine. Sherwood Gilbert and Piper, London. Vol 1. Accessed 200-06-17.
- British Medical Association. library periodical catalogue. Accessed 2007-06-17.
- Sylvanus Urban (July - December 1852). The Gentleman's Magazine and Historical review. John Bowyer, Nichols and Son, London. Page 167 sec. col. Accessed 2007-06-17
- Bassett, Judith. "Conolly, Edward Tennyson 1822 - 1908". Dictionary of New Zealand Biography. Ministry for Culture and Heritage. Retrieved 4 April 2011.
- Roberts, Andrew (1981) The 1832 Madhouse Act and the Metropolitan Commission in Lunacy from 1832 Middlesex University. Last accessed 28th June 2006
- ed: Bynum, W F; Porter, Roy; Shepard, Michael, ed. (1988). "Chapter 6". The anatomy of madness. Volume 3, The Asylum and its Psychiatry. London, England & New York, USA: Routledge. ISBN 0-415-00859-X.
- Universität Hamburg: The treatment of the insane without mechanical restraints. (1856) Historische texte zur behindertenpädagogik 22 Mb Tiff image document; last accessed 2006-09-17
-  Die Behandlung der Irren ohne mechanischen Zwang. Deutsch mitgetheilt von Dr. C.M. Brosius. Lahr, 1860 (Digitalisat)
- Scull, Andrew (c1989) Social Order/Mental Disorder: Anglo-American Psychiatry in Historical Perspective. John Conolly: A Victorian Psychiatric Career. Berkeley: University of California Press. Accessed 2007-09-21