The museum curates large collections of Plio-Pleistocene fossils, including hominids from Sterkfontein, Swartkrans and Kromdraai in the UNESCO World Heritage Site; the Cradle of Humankind, as well as late Permian therapsids (proto-mammals from the Karoo).

The most complete skull of an Australopithecus africanus specimen, Mrs Ples, is on display in the museum.

In addition, the Transvaal museum houses extensive collections of mammals, birds, reptiles, and invertebrates.

It was founded as the Staatsmuseum (Afrikaans for "State Museum") of the ZAR on 1 December 1892, and J. W. B. Gunning was appointed as its first director.

For the first two years after it was founded, the museum was located in the Ou Raadsaal parliament building.