The Garden was founded through a donation in 1791 by the historian and antiquarian Bengt Bergius and his brother Peter Jonas Bergius, a physician and scientist, for the Royal Swedish Academy of Sciences, and was originally located at their mansion and its adjacent garden on the Karlbergsvägen road, in what is now the Vasastaden district in central Stockholm. which at the time still had a largely rural character. The Garden was donated to the Royal Academy after the brothers' death in 1791, in accordance with their will. The first person to serve as director was Olof Swartz.
The garden was moved to its current location in 1885, because its original location was slated for construction. Today the garden is owned by the Swedish government and the Royal Swedish Academy of Sciences. It is jointly administered by the Academy of Sciences and Stockholm University.