Morton, who was born the son of a small farmer and village shopkeeper in Charlton City, Massachusetts, is believed to have trained as a dentist at the Baltimore College of Dentistry. After a brief partnership with Horace Wells, Morton set up in practice in Boston.

To alleviate the pain of tooth extraction Morton experimented with such drugs as opium and alcohol, but only succeeded in making his patients violently sick. The chemist Charles Jackson advised Morton to try ether, an old student standby, as a local anesthetic. This was moderately effective and Morton decided to try ether inhalation to produce general anesthesia. He first used ether to extract a tooth on 30 September 1860. His initial successes left Morton confident enough to offer to demonstrate his technique at the Massachusetts General Hospital. He was successful in using it on a patient who was undergoing a tumor operation. His innovation was well received by the leading surgeon John Warren and the use of ether quickly gained acceptance in medical practice. The news soon spread to Europe and in December 1846 Robert Liston, the skilled British surgeon, used ether in a painless and successful leg amputation at University College Hospital, London.

Morton subsequently went to a lot of trouble trying to patent his anesthetic and fight off competitors, notably Jackson, who were claiming priority. His wrangling with Jackson, the government, and the law courts achieved little and Morton died virtually penniless while traveling to New York to answer yet another attack on him from Jackson.