Van Allen was born at Mount Pleasant, Iowa. After graduating from the Iowa Wesleyan College in 1935 he went on to the University of Iowa, where he gained his PhD in 1939. His subsequent career took him to the Carnegie Institution of Washington (1939–42), as a physics research fellow in the department of terrestrial magnetism, and to the applied physics laboratory at the Johns Hopkins University (1942 and 1946–50). In 1951 Van Allen returned to the University of Iowa as a professor of physics and head of the department of physics and astronomy, retiring in 1990.

During the war years (1942–46) he served as an ordnance and gunnery specialist and combat observer with the US Navy and developed the radio proximity fuze, a device that guided explosive weapons, such as antiaircraft shells, close to their targets and then detonated them. He also gained considerable expertise in the miniaturization of electronics and rocket controls, which he later put to use in the scientific exploration of the Earth's upper atmosphere.

After the war Van Allen was able to use German V–2 rockets for atmospheric studies and was associated with the development of the Aerobee sounding rocket. He also used rocket–balloon combinations that could carry small rockets to higher altitudes. In the years 1949–57 he organized and led several scientific expeditions (to Peru, the Gulf of Alaska, Greenland, and Antarctica) to study cosmic rays – highly energetic particles arriving from space. The direction of all this work led to the launching in January 1958 of America's first satellite, Explorer I (as part of a major International Geophysical Year series of experiments), which carried experiments designed to measure cosmic rays and other energetic particles. Unexpectedly high radiation levels were found in certain regions of the Earth's atmosphere – so high that the satellite's Geiger counters jammed. This observation was contrary to the observation of the first Russian satellite, Sputnik I, launched five months earlier, and gave impetus to further satellite exploration. Subsequent observations by a succession of satellites (Explorer, Pioneer, Sputnik, Mechta, Lunik) have shown that the Earth's magnetic field traps high-speed charged particles in two zones girdling the Earth, with the greatest particle concentration above the equator. One zone lies roughly 600–3000 miles (1000–5000 km) above the Earth's surface; the other is 9000–15,000 miles (15,000–25,000 km) above the equator, curving down toward the magnetic poles. These regions were later to be named the Van Allen belts. The particles in the belts are electrons and protons (as suggested by F. Singer early in 1957) originating in cosmic-ray collisions or captured from the ‘solar wind’ of particles that streams out from the Sun. In 1958 a controversial experiment, known as ‘Project Argus’, was carried out – also as part of the International Geophysical Year. This involved the detonation of three small nuclear bombs, at altitudes over 300 miles (480 km) over the South Atlantic Ocean, to inject very energetic particles into the upper atmosphere. These were subsequently found to have been captured in the Van Allen belts.

Van Allen has produced over 200 scientific papers, has received a great number of scientific awards, and has been a member of several US governmental committees concerned with space exploration.