Tøyen i Aker was originally an estate owned by the Nonneseter Abbey. Norway's Chancellor Jens Bjelke acquired the property about 1620. King Frederik VI of Denmark later acquired the estate and subsequently gifted the property to the University of Christiania in 1812. In 1814, work began on the University Botanical Garden. The University of Oslo's oldest building, Tøyen Manor (Tøyen hovedgaard), is located in the garden. 
Johan Siebke was the botanical gardener at the Botanical Garden from the date of establishment. He contributed greatly to the planning and construction of the botanical garden and to the operation during the next first 40 years. The garden originally covered 75,000 square metres, but has since doubled in size. Botanical Museum (Botanisk museum) which dated to 1863 was merged with the Botanical Garden in 1975. The collection includes roughly 35,000 plants of about 7,500 unique species.