In 1884, Thomson became Cavendish Professor of Physics. In 1890, he married Rose Paget, and he had two children with her. One of his students was Ernest Rutherford, who would later succeed him in the post.

Thomson's discovery of the electron began in 1895 with a series of experiments in the Cavendish Laboratory. Influenced by the work of James Clerk Maxwell land the discovery of the X-ray, Thomson deduced that cathode rays (produced by Crookes tube) exhibited a single charge-to-mass ratio e m and must be composed of a single type of negatively charged particle, which he called "corpuscles." G. Johnstone Stoney had proposed the term electron earlier as a fixed quantum of electric charge in electrochemistry, but Thomson realized that it was also a subatomic particle, the first one to be discovered.

After further experiments on how cathode rays penetrate gases, Thomson hypothesized that "we have in the cathode rays matter in a new state this matter being the substance from which all the chemical elements are built up." Thomson might be described as "the man who first split the atom," and to a great extent, he made atom physics a modern science. He was awarded the Nobel Prize in Physics in 1906 and was knighted in 1908. His investigations into the action of electrostatic and magnetic fields in the nature of so-called "anode rays" or "canal rays" would eventually result in the invention of the mass spectrometer (then called a parabola spectrograph) by Francis Aston, a tool that allows the determination of the mass-to-charge ratio of ions and which has since become an ubiquitous research tool in chemistry.

Thomson was a gifted lecturer and teacher. His importance in physics is recognized almost as much for those he inspired as for his own experimental work. Seven Nobel Prizes were awarded to those who worked under him, including his son, Sir George Paget Thomson.

Prior to the outbreak of World War I, Thomson made another groundbreaking discovery: the isotope. He died on August 30, 1940, and was buried in Westminster Abbey, close to Isaac Newton.