The gardens, donated by the British royal family to the Yorkshire Philosophical Society in 1828, are located on part of the former site of St. Mary's Abbey. The society acquired the land to build a museum for its collections. The Yorkshire Museum was completed in 1830. The land was awarded to the Yorkshire Philosophical Society on the condition that botanical gardens be created on the site. These were designed in the garden style by the landscape architect Sir John Murray Naysmith in the 1830s. They originally contained a winter garden, pond and menagerie, which were destroyed when a bear escaped from it and briefly took control of the area. The then Princess Victoria visited the gardens in 1835, the year they were first opened to the public. In 1854 the gardens were described as "one of the chief attractions of York". At this time entry costs one shilling for members and one shilling for non-members, except on Saturday when it costs sixpence.
In 1960 the gardens and Yorkshire Museum were entrusted to the City of York Council and they became a public park. Since 2002 they have been managed by the York Museums Trust together with York Castle Museum and York Art Gallery. The gardens are maintained by the Askham Bryan College of Agriculture