Thompson's early work in electromagnetism led him to say, in 1893: "There is no other branch of physics which affords us so promising an opportunity of penetrating the secret of electricity." He turned his attention to cathode rays, and his subsequent investigations of these rays led him to the idea that they consisted of bodies smaller than atoms. Thomson's main contribution to science was the clear identification of the electron and its characterization as an elementary, subatomic particle in 1897. He showed that cathode rays were deflected by both magnetic and electric fields, and he was able to measure a cathode ray's charge/mass (e/m) ratio.

He was awarded the 1906 Nobel Prize in Physics for the discovery of the electron and his work on the conduction of electricity in gases.