The Royal Society was founded in 1660 to promote the new or experimental philosophy of that time, embodying the principles envisaged by Sir Francis Bacon. Henry Oldenburg was appointed as the first (joint) secretary to the Society and he was also the first editor of the Society's journal Philosophical Transactions. The Proceedings started out in 1800 as the Abstracts of the Papers Printed in the Philosophical Transactions of the Royal Society of London. The Royal Society published four volumes, from 1800 to 1843. Volumes 5 and 6, which appeared from 1843 to 1854, were called Abstracts of the Papers Communicated to the Royal Society of London. Starting with volume 7, in 1854, the Proceedings first appeared under the name Proceedings of the Royal Society of London. Publication of the proceedings in this form continued to volume 75 in 1905. Starting with volume 76, the Proceedings were split into Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character and Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character. The Proceedings have since undergone further name changes. Currently, the two series are called Proceedings of the Royal Society A — Mathematical, Physical & Engineering Sciences and Proceedings of the Royal Society B — Biological Sciences.

Proceedings A has an illustrious history of publishing pioneering and influential research articles across the range of the physical and mathematical sciences. These have included Maxwell's electromagnetic theory, the Braggs' first account of X-ray crystallography, Dirac's relativistic theory of the electron, and Watson and Crick's detailed description of the structure of DNA. Proc. R. Soc. A publishes refereed research articles in the mathematical, physical and engineering sciences. The emphasis is on high-quality, original, fundamental articles of interest to a wide range of scientists, in emerging and interdisciplinary areas as well as established disciplines. The journal is covered by the following index system: Applied Mechanics Reviews ,Bibliography and Index of Geology (Also known as GeoRef), British and Irish Archaeological Bibliography, Chemical Abstracts, Chemistry Citation Index, Composites Alert, Compumath Citation Index, Current Contents, Engineered, Materials Abstracts, Engineering Index Monthly, Excerpta Medica, Fluidex, Forest Products Abstracts , Geographical Abstracts, Human Geography , Geological Abstracts , Geomechanics Abstracts , Index to Scientific Reviews , INSPEC (The Institution of Electrical Engineers) (1968- ), Mass Spectrometry Bulletin , Mathematical Reviews , Metals Abstracts , Metals Abstracts Index , Mineralogical Abstracts , Nonferrous Metals Alert , Oceanographic Literature Review , Petroleum Abstracts , Polymers, Ceramics , Research Alert (Philadelphia) , Science Citation Index , Steels Alert , World Aluminum Abstracts.
The current Editor of the journal is Sir Michael Berry FRS.

This series covers research related to biological sciences. Topics covered in particular include ecology, behavioural ecology and evolutionary biology; significant numbers of papers in epidemiology, human biology, neuroscience, palaeontology and biomechanics have also appeared in the journal. The criteria for selection are scientific excellence, originality and potential interest to a wide spectrum of biologists. Proceedings B publishes predominately research articles but also publishes both commissioned and non-commissioned reviews, comments, replies and commentaries.
The current Editor of this section of the journal is Professor Michael Hassell FRS. The international editorial board dictating the direction of the journal, includes Professors and Doctors from major institutions such as The Royal Botanic Gardens Kew, University of Cambridge, Beijing Normal University, Imperial College London, Natural History Museum London and Princeton University.
In 2005, Biology Letters, (originally a supplement to Proceedings B), was launched as an independent journal to wide acclaim.