The Linnean Society was founded in 1788 by botanist Sir James Edward Smith. The society derives its name from the Swedish naturalist Carolus Linnaeus, the 'father of taxonomy', who systematised biological classification through his binomial nomenclature. He was known as Carl von Linné after his ennoblement, hence the spelling 'Linnean', rather than 'Linnaean'. The society had a number of minor name variations before it gained its Royal Charter on 26 March 1802, when the name became fixed as "The Linnean Society of London". In 1802, as a newly incorporated society, it comprised 228 fellows. It is the oldest extant natural history society in the world. Throughout its history the society has been a non-political and non-sectarian institution, existing solely for the furtherance of natural history.

The inception of the society was the direct result of the purchase by Sir James Smith of the specimen, book and correspondence collections of Linnaeus. When the collection was offered for sale by the heirs of Linnaeus, Smith was urged to acquire it by Sir Joseph Banks, the eminent botanist and president of the Royal Society. Five years after this purchase Banks gave Smith his full support in founding the Linnean Society, and he became one of the first Honorary Members of the new society.
The society has numbered many prominent scientists amongst its fellows. One such was the botanist Robert Brown, who was president (1849-1853); he named the cell nucleus and discovered Brownian motion. In 1854 Charles Darwin was elected a fellow; he is undoubtedly the most illustrious scientist ever to appear on the membership rolls of the society. Another famous fellow was biologist Thomas Huxley, who gained the nickname "Darwin's bulldog" for his outspoken defence of evolution. Men notable in other walks of life have also been fellows of the society, including the physician Edward Jenner, pioneer of vaccination, the Arctic explorers Sir John Franklin and Sir James Clark Ross, colonial administrator and founder of Singapore, Sir Thomas Stamford Raffles and Prime Minister of Britain, Lord Aberdeen.

Since 1857 the Society has been based at Burlington House, Piccadilly, London; an address it shares with a number of other learned societies: the Geological Society of London, the Royal Astronomical Society, the Society of Antiquaries of London and the Royal Society of Chemistry.

The first public exposition of the 'Theory of Evolution by Natural Selection', arguably the greatest single leap of progress made in biology, was presented to a meeting of the Linnean Society on 1 July 1858. At this meeting a joint presentation of papers by Charles Darwin and Alfred Russel Wallace was made, sponsored by Joseph Hooker and Charles Lyell as neither author could be present.

In 1904 the society experienced the novelty of electing women fellows; this followed a number of years of campaigning by the botanist Marian Farquharson. Whilst the society's council was reluctant to admit women, the fellows were much less so, with only 17% voting against the proposal. Among the first to benefit from this were: ornithologist and photographer Emma Louisa Turner, Lilian J. Veley, a microbiologist and Annie Lorrain Smith, a lichenologist and mycologist, all formally admitted on 19 January 1905. Also amongst the first women to be elected in 1904 was the paleobotanist, and later pioneer of family planning, Marie Stopes.

The society's connection with evolution remained strong into the 20th century. Sir Edward Poulton, who was president 1912-1916, was a great defender of natural selection and was the first biologist to recognise the importance of frequency-dependent selection.

The first female president of the society was Irene Manton (1973 to 1976), who pioneered the biological use of electron microscopy. Her work revealed the structure of the flagellum and cilia, which are central to many systems of cellular motility.

Recent years have seen an increased interest within the society in issues of biodiversity conservation. This was highlighted by the inception in 2015 of an annual award, the John Spedan Lewis Medal, specifically honouring persons making significant and innovative contributions to conservation.

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