 He was elected a Fellow of the Royal Society in 1847 and Goulstonian lecturer on dysentery at the Royal College of Surgeons the same year.Baly was killed in a railway accident near Wimbledon, southwest of London, on 28 January 1861; he is buried in the Kensal Green Cemetery, London.Baly was a fellow of the Royal College of Physicians of London, which awards a biennial Baly Medal in Physiology, in his name.