The Pretoria National Botanical Garden was established in 1946 when part of the University of Pretoria 's Experimental Farm and private properties along the northern part of the ridge were acquired by the Department of Agriculture. The Garden was initially known as the Transvaal National Botanic Gardens and could only be visited by special arrangement because it was primarily a research facility under the management of the Botanical Research Institute, which traces its origins back to 1903. The Institute amalgamated with the National Botanical Gardens of South Africa (Kirstenbosch) to form the National Botanical Institute in 1989, which in turn became the South African National Biodiversity Institute (SANBI) in 2004. The Garden was opened to the public on a daily basis in 1984.

The avenue of Bolusanthus trees planted by Mr Jan Evens in 1946 was one of the first plantings in the garden.

A small thatched stone building adjacent to the waterfall, which was previously used as the Botanical Tea Garden, was built in the late 1950s and initially served as the first office of the botanical garden.

Aloe Lodge, previously called Velcich House is situated on the northern side of the ridge running through the Pretoria National Botanical Garden . It was built in 1941 and was owned by Mr Antonio Velcich, who started the firm City Engineering in Mitchell Street , Pretoria . It is now used to accommodate visiting researchers.

Major infrastructure development has taken place since the 1990s and includes the construction of the Visitor's Centre, the Environmental Education Centre, Medicinal Garden , concert stage, artificial waterfall and lapa as well as the paving of the main walkways. Pretoria Portland Cement sponsored the artificial waterfall in 1993.

The old entrance gate depicting species of Aloe, named the Reynolds Gate in honour of Dr Gilbert Reynolds, who was an amateur botanist and an authority on Aloe plants, is permanently closed now and the new entrance is situated at the new Visitor Centre adjacent to this spectacular work of art. This beautiful wrought-iron artefact was designed and made by Hans Brugger. The other gate, also made by Mr Brugger, is the entrance to the Herbarium building and the new Biodiversity building on the rocky ridge of the garden.  

In 1947 a spectacular tree with a spreading crown, Acacia sieberiana var. woodii was planted near this gate by the first curator of the Garden, Mr A van der Ende. Unfortunately this tree collapsed in January 2005 after a period of heavy rain. This was the third tree to be planted in the Garden.

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