The YPS was formed in 1822 to pursue the study of natural sciences, and to combine the private collections of individual members.

In 1828 the Society was given a Royal Grant of some of the grounds which we now know as The Museum Gardens on which to build a museum to house the collections and create a botanic garden. The Society built the Yorkshire Museum in 1829 and continued rapidly to increase the collections, enhance and expand the Gardens, and to advance scholarship on scientific matters.

The British Association for the Advancement of Science (now known as The British Science Association) was founded with the help of the Society and had its inaugural meeting at the Yorkshire Museum in 1831. This was quickly followed by the building of an astronomical observatory in the Gardens, so continuing York's association with astronomical science.

The Tempest Anderson Hall was added to the Museum in 1912 as a bequest of the vulcanologist, Dr Tempest Anderson, to provide adequate facilities for scientific lectures.

In 1961, The Society handed the Museum and Gardens to the City of York in trust, but still continued to take an interest in them, as well as pursuing its objective of keeping members and the general public aware of scientific matters. The YPS continues to support the York Museums Trust through collaborations on projects and activities.

In 1971,  the Society joined the Council for British Archaeology in initiatives which led to the formation of the York Archaeological Trust.