Perrin was born in Lille, France, the son of an army officer. He was educated at the Ecole Normale, where he received his doctorate in 1897. He was appointed to the Sorbonne where he was made professor of physical chemistry in 1910. He remained there until 1941, when he went to America to escape the Nazis.

Perrin's early work was in the developing field of cathode rays and x-rays. In 1895 he established the important result that cathode rays are deflected by a magnetic field and thus carry a negative charge. He began to calculate the ratio of charge to mass for these particles but was anticipated by J. J. Thomson. In 1901 he produced a work on physical chemistry, Les Principes (Principles).

His most important work however was on Brownian motion and the molecular hypothesis. In 1828 Robert Brown had reported that pollen granules immersed in water moved continuously and erratically. However, it was left to Albert Einstein to provide some quantitative explanations for the motion in 1905. Assuming that the pollen was being moved by water molecules, he showed that the average distance traveled by a particle increased with the square of the elapsed time. Making the necessary corrections for temperature, size of particles, and nature of the liquid involved, Einstein made precise predictions about how far a particle should travel in a given time.

In 1908 Perrin was finally able to confirm Einstein's predictions experimentally. His work was made possible by the development of the ultramicroscope by Richard Zsigmondy and Henry Siedentopf in 1903. He was able to work out from his experimental results and Einstein's formula the size of the water molecule and a precise value for Avogadro's number.

The fundamental importance of this work was that it established atomism as something more than a useful hypothesis. It was mainly as a result of Perrin's work that the most eminent skeptic, Wilhelm Ostwald, at last relented. Perrin was awarded the Nobel Prize for physics in 1926 for his work on Brownian motion and sedimentation.

In 1913 he published Les Atomes (Atoms), which collected together not only his own work on molecules but new material from radiochemistry, black-body radiation, and many other fields, to demonstrate the reality of molecules. It was an enormously influential work, going through four editions in its first year and being translated into many languages.