Gunning was born at Swainswick and educated at Winchester. He was the assistant surgeon to St. George's Hospital, London, from 21 January 1760 to 4 January 1765, and full surgeon from that date till his death. In 1773 he was elected Steward of Anatomy by the Surgeons' Company, but paid a fine rather than serve. In 1789 he was elected Examiner on the death of Percivall Pott, and in the same year he was chosen Master of the Company, and signalised his year of office by a firm effort to reform its administration and reorganise its work. His attack upon the expensive system of dinners of the courts of assistants and of examiners, and his philippic on retiring from office on 1 July 1790, as recorded by South, show that he could be fearlessly outspoken. The Court of Assistants appointed a committee to consider the question, and numerous reforms were effected. In 1790 Gunning was appointed the first professor of surgery; but he soon resigned on the plea that it occupied too much of his time, and no new appointment was made. Gunning had been appointed Surgeon-General of the army in 1793, on the death of John Hunter; he was also senior Surgeon Extraordinary to the King.
Conflict with John Hunter
Gunning was in general opposed to his colleague at St. George's, John Hunter, who was frequently overbearing to his professional brethren, and appeared to them to neglect the proper business of a surgeon for unpractical pursuits. The quarrel rose to a great pitch when a surgeon was elected in succession to Charles Hawkins, who had resigned. Thomas Keate was supported by Gunning, and Everard Home by Hunter, and after a sharp contest Keate was elected. A dispute ensued about fees for surgical lectures, which led to a controversy between Gunning, senior surgeon, supported by two of his colleagues, and Hunter. It ended in John Hunter's dramatically sudden death on 16 Oct. 1793, immediately after being flatly contradicted by one of his colleagues, apparently Gunning.
In 1796 it was determined to sell the Surgeons' Hall on account of the expense attending its repair; but on 7 July Gunning, on behalf of the committee, reported that as no one had bid within £200 of the price set upon it, it had been bought in. At the same court Henry Cline was elected a member of the Court of Assistants, in the absence of a governor. This voided the charter. A bill brought into parliament in 1797 to indemnify the company, and to give it greater power over the profession, after passing the commons, was lost in the House of Lords by the influence of Thurlow, owing, it is said, to a grudge against Gunning. Thurlow having said, "There's no more science in surgery than in butchery". Gunning had retorted: "Then, my lord, I heartily pray that your lordship may break your leg, and have only a butcher to set it". Gunning died at Bath on 14 Feb. 1798, leaving five children.