With the outbreak of World War II, the proximity fuze work was transferred to the newly created Applied Physics Laboratory (APL) of Johns Hopkins University in April 1942.

Van Allen was commissioned as a U.S. Navy lieutenant in November 1942 and served for 16 months on a succession of South Pacific Fleet destroyers, instructing gunnery officers and conducting tests on his artillery fuses.

He was an assistant staff gunnery officer on the battleship USS Washington when the ship successfully defended itself against a Japanese attack during the Battle of the Philippine Sea, (June 19–20, 1944).

He organized and directed a team at Johns Hopkins University to conduct high-altitude experiments, using V-2 rockets captured from the Germans at the end of World War II.

The first instrument-carrying Aerobee was the A-5, launched on March 5, 1948, from White Sands, New Mexico, carrying instruments for cosmic radiation research, reaching an altitude of 117.5 km.

Van Allen developed the idea for the Rockoon on March 1, 1949, during the Aerobee rocket firing cruise on the research vessel USS Norton Sound.

Before long, he was enlisting students in his efforts to discover the secrets of the wild blue yonder and inventing ways to carry instruments higher into the atmosphere than ever before.

On the theory that extreme cold at high altitude might have stopped the clockwork supposed to ignite the rockets, Van Allen heated cans of orange juice, smuggled them into the third Rockoon’s gondola, and wrapped the whole business in insulation.

Van Allen got on the phone, soon gathered eight or ten top scientists (Lloyd Berkner, S. Fred Singer, and Harry Vestine) in the living room of his small brick house.

The talk turned to geophysics and the two ‘International Polar Years’ that had enlisted the world’s leading nations to study the Arctic and Antarctic regions in 1882 and 1932.

From this meeting Lloyd Berkner and other participants proposed to the International Council of Scientific Unions that an IGY be planned for 1957–58 (during the maximum solar activity)....

[15] A symposium on "The Scientific Uses of Earth Satellites" was held on January 26 and 27, 1956 at the University of Michigan under sponsorship of the Upper Atmosphere Rocket Research Panel, chaired by Dr. Van Allen.

The May 4, 1959, issue of Time magazine credited James Van Allen as the man most responsible for giving the U.S. "a big lead in scientific achievement."

[22] Abigail M. Foerstner wrote a biography James van Allen: The First Eight Billion Miles, published by University of Iowa Press in 2007 with a paperback edition in 2009.

[31] Managed by NASA's Goddard Space Flight Center[31] and implemented by the Applied Physics Laboratory (APL) at Johns Hopkins University,[32] the mission was a part of the Living With a Star program.

Designed for a two-year primary mission, the probes exceeded expectations by operating for seven years, demonstrating significant resilience against radiation in Earth's belts.

[32] In collaboration with the Balloon Array for RBSP Relativistic Electron Losses (BARREL), the probes studied particles from the belts reaching Earth's atmosphere.

Key discoveries included the dynamics of the Van Allen radiation belts and the role of solar activity in influencing space weather.

The mission's findings highlighted how these radiation belts swell and shrink over time, responding to solar eruptions and impacting terrestrial phenomena like auroras, satellite functionality, power grids, and GPS communications.

During geomagnetic storms, the enhancement of the ring current was shown to be due to low-energy protons entering the near-Earth region, challenging previous understandings.

[38] Eighty years after the Second Byrd Expedition, the Balloon Array for RBSP Relativistic Electron Losses (BARREL), a NASA mission began to study Earth's Van Allen radiation belts at the Antarctic (South Pole) managed by Dartmouth College.