[3][1] He was educated under Charles Chalmers at Merchiston Castle School, then from 1845 studied medicine at the University of Edinburgh graduating with an MD.

In 1868 he assumed the duties of professor of botany at the Royal College of Science, Dublin, and finally in 1870 he received the natural history chair at the University of Edinburgh.

[4] The remarkable hydrographic and zoological results which Thomson had demonstrated, in addition to the growing demands of ocean telegraphy, soon led to the Royal Navy to grant use of HMS Challenger for a global expedition.

[7] The Challenger expedition was deemed a great success, and on his return Thomson received a number of academic honours, as well as a knighthood.

In 1879 he ceased to perform his university duties, gave up overseeing the reports of the expedition in 1881 (after publishing the introduction to the zoological series in 1880),[1] then took to his bed and died a broken man at Bonsyde on 10 March 1882.

[4] Thomson's friend and colleague Sir John Murray took over the publication of the reports; they eventually spanned 50 volumes, the last of which was issued in 1895.

[1] Thomson is commemorated in the stained glass window above the altar in St. Michael's Parish Church, Linlithgow and his headstone is in the churchyard.