Joseph John Thomson was born 18 December 1856 in Cheetham Hill, Manchester, Lancashire, England. His mother, Emma Swindells, came from a local textile family. His father, Joseph James Thomson, ran an antiquarian bookshop founded by a great-grandfather. He had a brother, Frederick Vernon Thomson, who was two years younger than he was. J. J. Thomson was a reserved yet devout Anglican.

His early education was in small private schools where he demonstrated outstanding talent and interest in science. In 1870 he was admitted to Owens College in Manchester (now University of Manchester) at the unusually young age of 14. His parents planned to enroll him as an apprentice Engineer to Sharp-Stewart & Co, a locomotive manufacturer, but these plans were cut short when his father died in 1873.

He moved on to Trinity College, Cambridge, in 1876. In 1880 he obtained his Bachelor of Arts degree in mathematics (Second Wrangler in the Tripos and 2nd Smith's Prize). He applied for and became a Fellow of Trinity College in 1881. Thomson received his Master of Arts degree (with Adams Prize) in 1883.

Thomson was elected a Fellow of the Royal Society on 12 June 1884 and served as President of the Royal Society from 1915 to 1920.

Much of his work in mathematical modelling of chemical processes can be thought of as early computational chemistry. In further work, published in book form as Applications of dynamics to physics and chemistry (1888), Thomson addressed the transformation of Energy in mathematical and theoretical terms, suggesting that all Energy might be kinetic. His next book, Notes on recent researches in electricity and magnetism (1893), built upon Maxwell's Treatise upon electricity and magnetism, and was sometimes referred to as "the third volume of Maxwell". In it, Thomson emphasized physical methods and experimentation and included extensive figures and diagrams of apparatus, including a number for the passage of electricity through gases. His third book, Elements of the mathematical theory of electricity and magnetism (1895) was a readable introduction to a wide variety of subjects, and achieved considerable popularity as a textbook.

In 1890, Thomson married Rose Elisabeth Paget, one of his former students, daughter of Sir George Edward Paget, KCB, a physician and then Regius Professor of Physic at Cambridge at the church of St. Mary the Less. They had one son, George Paget Thomson, and one daughter, Joan Paget Thomson.

A series of four lectures, given by Thomson on a visit to Princeton University in 1896, were subsequently published as Discharge of electricity through gases (1897). Thomson also presented a series of six lectures at Yale University in 1904.

In April 1897, Thomson had only early indications that the cathode rays could be deflected electrically (previous investigators such as Heinrich Hertz had thought they could not be). A month after Thomson's announcement of the corpuscle, he found that he could reliably deflect the rays by an electric field if he evacuated the discharge tube to a very low pressure. By comparing the deflection of a beam of cathode rays by electric and magnetic fields he obtained more robust measurements of the mass-to-charge ratio that confirmed his previous estimates. This became the classic means of measuring the charge and mass of the electron.

Thomson believed that the corpuscles emerged from the atoms of the trace gas inside his cathode ray tubes. He thus concluded that atoms were divisible, and that the corpuscles were their building blocks. In 1904 Thomson suggested a model of the atom, hypothesizing that it was a sphere of positive matter within which electrostatic forces determined the positioning of the corpuscles. To explain the overall neutral charge of the atom, he proposed that the corpuscles were distributed in a uniform sea of positive charge. In this "plum pudding" model the electrons were seen as embedded in the positive charge like plums in a plum pudding (although in Thomson's model they were not stationary, but orbiting rapidly).

In 1905, Thomson discovered the natural radioactivity of potassium.

In 1906, Thomson demonstrated that hydrogen had only a single electron per atom. Previous theories allowed various numbers of electrons.

In 1912, as part of his exploration into the composition of the streams of positively charged particles then known as canal rays, Thomson and his research assistant F. W. Aston channelled a stream of neon ions through a magnetic and an electric field and measured its deflection by placing a photographic plate in its path. They observed two patches of light on the photographic plate (see image on right), which suggested two different parabolas of deflection, and concluded that neon is composed of atoms of two different atomic masses (neon-20 and neon-22), that is to say of two isotopes. This was the first evidence for isotopes of a stable element; Frederick Soddy had previously proposed the existence of isotopes to explain the decay of certain radioactive elements.

In November 1927, J.J. Thomson opened the Thomson building, named in his honour, in the Leys School, Cambridge.

One of Thomson's greatest contributions to modern science was in his role as a highly gifted Teacher. One of his students was Ernest Rutherford, who later succeeded him as Cavendish Professor of Physics. In addition to Thomson himself, six of his research assistants (Charles Glover Barkla, Niels Bohr, Max Born, william Henry Bragg, Owen Willans Richardson and Charles Thomson Rees Wilson) won Nobel Prizes in physics, and two (Francis william Aston and Ernest Rutherford) won Nobel prizes in chemistry. In addition, Thomson's son (George Paget Thomson) won the 1937 Nobel Prize in physics for proving the wave-like properties of electrons.

He was awarded a Nobel Prize in 1906, "in recognition of the great merits of his theoretical and experimental investigations on the conduction of electricity by gases." He was knighted in 1908 and appointed to the Order of Merit in 1912. In 1914 he gave the Romanes Lecture in Oxford on "The atomic theory". In 1918 he became Master of Trinity College, Cambridge, where he remained until his death. Joseph John Thomson died on 30 August 1940; his ashes rest in Westminster Abbey, near the graves of Sir Isaac Newton and his former student, Ernest Rutherford.

In 1991, the thomson (symbol: Th) was proposed as a unit to measure mass-to-charge ratio in mass spectrometry in his honour.

Thomson constructed a Crookes tube with a better vacuum. At the start of the tube was the cathode from which the rays projected. The rays were sharpened to a beam by two metal slits – the first of these slits doubled as the anode, the second was connected to the earth. The beam then passed between two parallel aluminium plates, which produced an electric field between them when they were connected to a battery. The end of the tube was a large sphere where the beam would impact on the glass, created a glowing patch. Thomson pasted a scale to the surface of this sphere to measure the deflection of the beam. Note that any electron beam would collide with some residual gas atoms within the Crookes tube, thereby ionizing them and producing electrons and ions in the tube (space charge); in previous experiments this space charge electrically screened the externally applied electric field. However, in Thomson's Crookes tube the density of residual atoms was so low that the space charge from the electrons and ions was insufficient to electrically screen the externally applied electric field, which permitted Thomson to successfully observe electrical deflection.