Bell studied medicine at the University of Edinburgh Medical School and received an MD in 1859 presenting the thesis "Epithelial cancer: its pathology and treatment".

He was buried at the Dean Cemetery in Edinburgh alongside his wife Edith Katherine (or Catherine) Erskine Murray (1840–1874) and their son Benjamin, and next to his parents' and brother's plots.

The couple had five children, of whom only three survived infancy: Arthur Conan Doyle met Bell in 1877, and served as his clerk at the Edinburgh Royal Infirmary.

The BBC television series Murder Rooms: The Dark Beginnings of Sherlock Holmes was a fictionalized account of Doyle's time as Bell's clerk.

The original one-off production, which led to the later series, was released on DVD and VHS in the US in 2003, titled Dr. Bell and Mr. Doyle – The Dark Beginnings of Sherlock Holmes.

In episode 14 of the show's eighth and final season, House briefly comes to believe that his biological father is a man named Thomas Bell, played by prominent Scottish actor Billy Connolly.

A bronze plaque memorial was erected to Joseph Bell at 2 Melville Crescent in Edinburgh, his home for his final decades, on 8 October 2011, the centenary of his death.

The unveiling ceremony was attended by the several people involved in the erection of the plaque (principally Takeshi Shimizu) and representatives of various Sherlock Holmes clubs and societies.