Born at Zonnemair in the Netherlands, Zeeman studied at Leiden University and received a doctorate in 1893. This was for his work on the Kerr effect, which concerns the effect of a magnetic field on light. In 1896 he discovered another magnetooptical effect, which now bears his name – he observed that the spectral lines of certain elements are split into three lines when the sample is in a strong magnetic field perpendicular to the light path; if the field is parallel to the light path the lines split into two. This work was done before the development of quantum mechanics, and the effect was explained at the time using classical theory by Hendrik Antoon Lorentz, who assumed that the light was emitted by oscillating electrons.

This effect (splitting into three or two lines) is called the normal Zeeman effect and it can be explained using Niels Bohr's theory of the atom. In general, most substances show an anomalous Zeeman effect, in which the splitting is into several closely spaced lines – a phenomenon that can be explained using quantum mechanics and the concept of electron spin.

Zeeman was a meticulous experimenter and he applied his precision in measurement to the determination of the speed of light in dense media, confirming Lorentz's prediction that this was related to wavelength. Also, in 1918, he established the equality of gravitational and inertial mass thus reconfirming Einstein's equivalence principle, which lies at the core of general relativity theory.

Zeeman and Lorentz shared the 1902 Nobel Prize for physics for their work on magnetooptical effects.