He obtained his medical degree in 1851 with the highest honours in anatomy and surgery[1] and set up a practice at 35 Wimpole Street in London, where he lived and worked until his death in 1904.

[2] In 1863, when King Leopold I of Belgium was suffering from kidney stones, Thompson was called to Brussels to consult in the case, and after some difficulties was allowed to perform the operation of lithotripsy.

He denounced the prevailing methods of death certification in Great Britain; and in 1892 a select committee was appointed to inquire into the matter; its report, published the following year, was generally in line with his thinking.

[8] Thompson was also an artist, producing sketches and paintings, some of which were hung at the Royal Academy of Arts and in the Paris Salon.

[4] Sir Henry Thompson, knighted in 1867, received a baronetcy in 1899, in connection with his telescope gifts to the National Observatory.

Of his two daughters, the elder Kate Mary Margaret Thompson (1856–1942) was the author of a valuable Handbook to the Public Picture Galleries of Europe, first published in 1877.

They had two sons, the youngest was the World War I poet Alec de Candole[10] Thompson believed in an impersonal God.

[15] The Royal College of Surgeons in 1852 awarded Thompson the Jacksonian Prize for an essay on the Pathology and Treatment of Stricture of the Urethra (on stenosis of the urethra, a common condition in the times of gonorrhea and other sexually transmitted diseases); and again in 1860 for his essay on the Health and Morbid Anatomy of the Prostate Gland.

[1] Besides devising operative improvements, he wrote books and papers dealing with them, including:[4] He produced two successful novels, Charley Kingston's Aunt (1885) and All But (1886).