Van der Meer was educated at the Gymnasium in his native city of The Hague and at the Technical University, Delft, where he gained his PhD in 1956. He immediately joined the staff at the European Organization for Nuclear Research (CERN) and remained there until his retirement in 1990.

In 1979 the Nobel Prize for physics was awarded to Sheldon Glashow and two colleagues for their unification of the electromagnetic and weak forces. Although the neutral currents predicted by the theory were detected in 1973, it still remained to discover the charged W⁺ and W^– and the neutral Z⁰ bosons whose existence was a consequence of the theory. As the masses of the particles were about 80 times that of the proton, the energy required for their production outstripped the capacity of any existing accelerator. In 1978 Carlo Rubbia, a colleague at CERN, asked van der Meer if there was any way to conjure such high energies from the existing accelerators.

CERN's SPS (Super Proton Synchroton) could deliver about 450 billion electronvolts (450 GeV). One possible solution would be to convert the SPS into a colliding-beam machine, that is, protons and antiprotons would be accelerated, stored separately, and then induced to collide with each other head-on. Proton–antiproton collisions, it was calculated, with an energy of 270 GeV per beam were equivalent to a beam of 155,000 GeV hitting with a stationary target.

The problem facing van der Meer was how to concentrate the beams. Protons normally repel each other, as do antiprotons, and, consequently, charged particle beams tend to spread out in space. To maximize the colliding power of the beams van der Meer somehow needed to focus them. He proposed to use the technique of ‘stochastic cooling’, first described by him in 1972 as a way of reducing random motion in the beam. To achieve this the exact center of the beam was calculated and correcting magnetic fields were applied by a system of ‘kickers’ placed around the ring. By this means particles out of line were nudged back into position. The system was successfully tested in May 1979 and was used in 1983 to create the W and the Z particles. Van der Meer shared the 1984 Nobel Prize for physics with Rubbia for this work.