Courtois was the son of a saltpeter manufacturer from Dijon in France and as a small boy he worked in the plant showing an alert interest. He was later apprenticed to a pharmacist and subsequently studied at the Ecole Polytechnique under Antoine Fourcroy. During his military service as a pharmacist he became the first to isolate morphine in its pure form from opium.

Meanwhile his father's saltpeter business had been running into difficulties because the product could be manufactured more cheaply in India, and Courtois returned to help his father. Saltpeter was obtained from the seaweed washed ashore in Normandy; the ashes (known as ‘varec’) were leached for sodium and potassium salts. Courtois noticed that the copper vats in which the lye was stored were becoming corroded by some unknown substance. By chance, in 1811, during the process of extracting the salts, he added excess concentrated sulfuric acid to the lye (the solution obtained by leaching) and was astonished to see “a vapor of a superb violet color” that condensed on cold surfaces to form brilliant crystalline plates. Courtois suspected that this was a new element but lacked the confidence and the laboratory equipment to establish this and asked Charles Bernard Désormes (1777–1862), the discoverer in 1801 of carbon dioxide, to continue his researches. His discovery was announced in 1813, and Joseph-Louis Gay-Lussac and Humphry Davy soon verified that it was an element, Gay-Lussac naming it iodine (from the Greek for ‘violet’).