The journal was established as the Journal of the Chemical Society A: Inorganic, Physical, Theoretical in 1966. In 1972, the journal was divided into three separate journals: Journal of the Chemical Society, Dalton Transactions (covering inorganic and organometallic chemistry), Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases, and Journal of the Chemical Society, Faraday Transactions 2: Molecular and Chemical Physics. The journal obtained its current name in 2003. In January 2000, Acta Chemica Scandinavica was absorbed.
The Journal of the Chemical Society, Dalton Transactions was published as 12 issues a year from 1972. As submissions increased, the journal switched to 24 issues a year in 1992 and then to 48 issues a year in 2006.
In 2010, the journal introduced a sequential volume numbering scheme, with one volume per year. While volume numbers were not assigned retro-actively, the first issue of 2010 was assigned volume 39 (2010 being the 39th year since the establishment of the Journal of the Chemical Society, Dalton Transactions.