Thomson, who was born in Manchester, entered Owens College (later Manchester University) at the age of 14. After studying engineering and then the sciences, he won a scholarship to Trinity College, Cambridge University. He graduated in 1876 and remained a member of the college in various capacities for the rest of his life. After graduating he worked at the Cavendish Laboratory under John Rayleigh, whom he succeeded as Cavendish Professor of Experimental Physics in 1884. As professor, Thomson built up the Cavendish Laboratory as a great and primarily experimental research school. Thomson was succeeded as professor in 1919 by his student Ernest Rutherford.

Thomson's most brilliant and famous scientific work was his investigations into cathode rays, in which he is considered to have discovered the electron. Using a highly evacuated discharge tube he calculated the velocity of the rays by balancing the opposing deflections caused by magnetic and electric fields. Knowing this velocity, and using a deflection from one of the fields, he was able to determine the ratio of electric charge (e) to mass (m) of the cathode rays. Thomson found that the ratio e/m was the same irrespective of the type of gas in the tube and the metal of the cathode, and was about a thousand times smaller than the value already obtained for hydrogen ions in the electrolysis of liquids. He later measured the charge of electricity carried by various negative ions and found it to be the same in gaseous discharge as in electrolysis. He thus finally established that cathode rays were negatively charged particles, fundamental to matter, and much smaller than the smallest atoms known. This opened up the way for new concepts of the atom and for the study of subatomic particles. Thomson announced his discovery of a body smaller than the hydrogen atom in April 1897.

His later researches included studies of Eugen Goldstein's canal rays, which he named positive rays. These studies gave a new method (1912) of separating atoms and molecules by deflecting positive rays in magnetic and electric fields. Ions of the same charge-to-mass ratio form a parabola on a photographic plate. Using this arrangement, Thomson first identified the isotope neon–22. This work was taken up by Francis W. Aston, who later developed the mass spectrograph.

Thomson's treatises were widely used in British universities. His Conduction of Electricity Through Gases (1903) describes the work of his great days at the Cavendish; his autobiography, Recollections and Reflections, was published in 1936. He was awarded the 1906 Nobel Prize for physics for his work on the conduction of electricity through gases, and was knighted in 1908.