They were created shortly after the university's reform in 1539, when Maurice, Elector of Saxony donated the Dominican monastery of St. Pauli.
In 1876–1877, after the decision to erect a court house on its site, the garden was relocated once again to its present location southeast of Leipzig.
The garden was utterly destroyed in World War II, with the ruins of the Botanical Institute subsequently demolished and backfilled with rubble.
The garden contains a systematic department, as well as geographic arrangements of plants from the steppes of Eastern Europe and Asia, forests of the northern hemisphere, prairies, and eastern North America, as well as a marsh and pond with regional flora and an alpine garden containing plants from Asia, Europe, and South America.
Its greenhouses (2,400 m2 total area) contain plants from subtropical and tropical zones of the Mediterranean region, Africa, Central America, and Australia.