The Bergius Botanic Garden was started by two brothers, Peter Jonas and Bengt Bergius. Their seven hectare property called Bergielund, located between Karlbergs allé (today's Karlbergsvägen) and Vasaparken in central Stockholm, was developed as a horticultural school. Following their death in the late 18th century the property was donated to the Royal Swedish Academy of Sciences (external link, opens in new window). This was the starting point of the Bergius Foundation, established in 1791.

In 1885 the garden was transferred to its present location in Frescati where the Professor Bergianus at the time,  the botanist Veit Wittrock, developed a new garden following scientific principles. The plants were now arranged according to their classification and geographical origin. The Bergius Foundation is today primarily a research institution at the Royal Swedish Academy of Sciences, but is also responsible for the Edvard Anderson Conservatory in the garden.

The outside areas of the garden, the Victoria greenhouse, and the tropical sections of the Edvard Anderson Conservatory are today owned and managed by Stockholm University (external link, opens in new window).