The garden was first mentioned by university recordings already in 1467. At the time, the area was twice as large as today, stretching from the southwestern side of Collegium Maius to the city wall. Initially it was a garden and an orchard providing fresh fruit and vegetables for the professors' tables in the college's refectory. In 1475, a large poultry pen was built here. From 1510 the garden had latrines connected to the sewage system, used by students and scholars who lived in the Collegium.
Near to the end of 18th century, as a result of the University's reforms, the garden was left to neglect by the professors. During the Collegium Maius restoration (1840-1871), the University authorities did not decide to have it renewed. The garden served as a place for storage of construction materials. It wasn't before the late 19th century when the garden was taken over by the Department of Botanic and for a certain time used to grow ca. 300 plant species. Due to the construction of the Collegium Witkowskiego in the early 20th century, the garden was destroyed and remained in state of neglect until the 1960s. Although it was partially tidied up after the post-war reconstruction of Collegium Maius, soon it would again become the backyard for restoration works.
In the years 2008-2010 the Public Committee for Restoration of Cracow Monuments financed a reconstruction of the Professor Garden and Jagiellonian University. On 12th May 2010 the Garden was officially made available for visitors. The restoration works included creation of paved alleys and benches, as well as planting of bushes, flowers and wild strawberries. Additional attractions in this area are sculptures presenting University professors and modern educational installations, e.g. a sundial and a model of armillary sphere. While visiting the Garden, one is able to admire recently renewed facades of surrounding historical buildings. During the summer season, due to increased number of visitors, another entrance is available from the courtyard, the "Long Hallway".