A laboratory has existed on the Chilton site since 1957 when the then Rutherford High Energy Laboratory, an establishment of the National Institute for Research in Nuclear Science (NIRNS), was set up.

In 1965, as part of a government re-structuring of scientific research bodies, the Science Research Council (SRC) which took over management of the Rutherford High Energy Laboratory from NIRNS along with many other UK science bodies.

The Rutherford Laboratory merged with the Atlas Computer Laboratory and Appleton Laboratories in 1975 and 1979 respectively. The Laboratory was re-named after the physicists Ernest Rutherford and Edward Appleton. In 1998, with the closure of the Royal Greenwich Observatory, some of its offices became part of RAL. The foundations of the the Laboratory's Central Laser Facility were laid when laser technology moved from Joint European Torus at Culham into RAL.

RAL’s has undertaken pioneering work in areas such as particle physics, scientific computing, laser development, space research, and technology.

As of 2018, approximately 1200 staff work on site. The site is funded and managed by the Science and Technology Facilities Council (STFC).