The Botanical Garden were previously situated east of the Fyris river, where the Linnaeus Garden is today. The location of the garden close to the river led to many floodings. By the late 1700s, the garden had also become overcrowded. Carl Peter Thunberg, an apostle of Linnaeus and successor, was able to convince Gustaf III of Sweden to donate the garden of Uppsala Castle to the university in 1787, to be used as Botanical Garden.
By 1807, all of the plants had been moved to the new garden opened on 21 May, 100 years after Linneaus' birth. The castle garden was designed in the Baroque style by architect Carl Hårleman in the 1750s. The king also donated money for the construction of the Linnaeanum, the building which houses the Botanical Garden's Orangery.
Both the Baroque Garden and the Linnaeanum are listed property. According to Gustav III's deed of donation, the Baroque Garden must be kept in the same condition as when it was donated. An extensive restoration in accordance with Hårleman's original plans was carried out in 1974.
During the 19th and 20th centuries, the Botanical Garden has been extended a number of times and new, more functional greenhouses have been added. The garden's primary purpose is still to serve the research and academic communities. Over time, it has become ever more open to the public and taken on more purposes, such as the conservation of biodiversity. The gardens also function today as a living plant museum with more than 100,000 visitors each year.