His father wished him to enter business, but circumstances ultimately enabled him to follow his own desire of becoming a physician, and in 1848 he entered the Medical School of University College London. There he had a brilliant career, and obtained his degree at London University in 1851 with the highest honors in anatomy and surgery. In 1851 he married Miss Kate Loder, a talented pianist, who, though stricken with paralysis soon afterwards, was always a devoted helpmate to him. In 1853 he was appointed assistant surgeon at University College Hospital, becoming full surgeon in 1863, professor of clinical surgery in 1866, and consulting surgeon in 1874. In 1884 he became professor of surgery and pathology in the Royal College of Surgeons, which in 1852 had awarded him the Jacksonian Prize for an essay on the Pathology and Treatment of Stricture of the Urethra (on stenosis of the urethra, a very common condition in the times of gonorrhea and other sexually transmitted diseases), and again in 1860 for another on the Health and Morbid Anatomy of the Prostate Gland. These two memoirs indicate the medical specialty to which he devoted his main attention, namely urology. Specializing in the surgery of the genito-urinary tract, and in particular in that of the bladder, he went to Paris to study under Jean Civiale (1796-1867), who in the first quarter of the 19th century proved that it is possible to crush a stone within the human bladder and invented the first surgical instrument for this minimally invasive surgery. After his return he soon acquired a high reputation as a skilful operator in that class of disease.
In 1863, when the King of Belgium was suffering from kidney stones, he was called to Brussels to consult in the case, and after some difficulties was allowed to perform the operation of lithotripsy: this was quite successful, and in recognition of his skill Thompson was appointed surgeon-extraordinary to the King, an appointment which was continued by Léopold II. Nearly ten years later he carried out a similar operation on the former Emperor Napoléon III; however, the Emperor died four days after, not from the surgical interference, as was proved by the post-mortem examination, but from uremia.
Besides devising various operative improvements in the treatment of the disorders which were his speciality, Sir Henry Thompson wrote various books and papers dealing with them, including Clinical Lectures on Diseases of the Urinary Organs, Practical Lithotomy and Lithotrity, Tumours of the Bladder, Suprapubic Lithotomy, and Preventive Treatment of Calculus Disease. Among other books of a medical character that came from his pen were Food and Feeding, and Diet in Relation to Age and Activity, both of which passed through a number of editions.
In 1874 he took a foremost part in founding the Cremation Society of Great Britain, of which he was the first president; and not only was he active in urging the advantages of cremation as a means of disposing of the body after death, but also did much towards the removal of the legal restrictions by which it was at first sought to prevent its practice in England. On various occasions he denounced the slackness and inefficiency of the methods of death certification prevalent in Great Britain, and in 1892 his agitation was instrumental in procuring the appointment of a select committee to inquire into the matter; its report, published in the following year, in great measure confirmed his criticisms and approved the remedies he suggested.
But medicine and hygiene by no means exhaust the list of Sir Henry Thompson's activities. In art he was an accomplished sketcher and, moreover, an amateur of painting whose pictures were hung at the Royal Academy of Arts and in the Paris Salon. About 1870 he began to get together his famous collection of Chinese porcelain, in particular of old blue and white Nanking; this in time became so large that he could no longer find room for it, and most of it was sold. A catalogue of it, illustrated by himself and James Whistler, was published in 1878.
He became also notorious in the art of gastronomy. In his famous "octaves" he was said to have elevated the giving of dinner parties into a fine art. The number of courses and of guests was alike eight, and both were selected with the utmost care and discrimination to promote the "feast of reason and the flow of soul."
In literature, in addition to more serious works, he produced two novels, Charley Kingston's Aunt (1885) and All But (1886), which met with considerable success.
In science he became a devotee of astronomy, and for a time maintained a private astronomical observatory in his house at Molesey. He further did much to promote astronomical study in Great Britain by presenting Royal Greenwich Observatory with some of the finest instruments now among its equipment, his gifts including a photographic heliograph of 9-inch aperture; a 30-inch reflecting telescope, and a large refracting telescope having an object glass of 26 inches of diameter and a focal length of 22 feet. The offer of the last instrument was made in 1894. Its manufacture was undertaken by Sir Howard Grubb of Dublin, and its erection was completed in 1897. It added greatly to the instrumental resources of Greenwich, especially for photographic work, and its importance may be gauged from the fact that both in aperture and focal length it is double the size of any instrument possessed by the observatory at the time it was put in place.
Thompson died on April 18 1904. His family consisted of an only son, Herbert, a barrister and well-known egyptologist, who succeeded to the baronetcy, and two daughters, of whom the elder (author of a valuable Handbook to the Public Picture Galleries of Europe, first published in 1877), married Archdeacon Watkins of Durham, and the younger one married the Rev. H. de Candole.