The science of botany for medical purposes was taught at the Jagiellonian University from the end of the 16th century, but the university did not have its own research garden. Rector Kazimierz Stępowski in 1756 allocated 5,000 zlotys for preliminary works on the establishment of the garden. This idea was reinforced by the university reform carried out by Hugo Kołłątaj. The beginning of the establishment of the Krakow botanical garden dates back to 1779, when King Stanisław August Poniatowski gave the post-Jesuit lands on Wesoła street, where the Botanical Garden is located to this day.
The first works on establishing the garden began in 1783, the first greenhouses were built in 1787, in 1865 the greenhouse was rebuilt, and in 1866 the construction of the wall separating the garden from Grzegórzki was completed. A large palm house was built in 1882. The garden is considered a monument and therefore it is subject to strict protection, and its most valuable monument is the Jagiellonian Oak – a remnant of the Nadwiślańska forest. In the garden, there are decorations from famous botanists and distinguished naturalists, such as B. Pawłowski, J. Warszewicz, M. Raciborski and others.