On 2 January 1922, Dr E.C.N. van Hoepen was appointed as the first full-time Director of the National Museum. He was appointed mainly on the grounds of his qualifications and "more especially, as it had been suggested by Government, that this Museum should specialize in Palaeontology". This represented a new phase in the development of the Museum. During Van Hoepen's term of office, emphasis was placed on research, especially palaeontological and archaeological research and the National Museum developed into an internationally recognized research institution. The Museum buildings were extended with the addition of two new wings, an office block and workrooms. Dr van Hoepen retired in 1950.

When Dr A.C. Hoffman was appointed Director in April 1951, the entire staff consisted of Hoffman and five assistants. At the end of his tenure as Director, the staff complement had increased to 23. Hoffman placed great emphasis on the educational function of the Museum and on his initiative excellent displays and dioramas were completed. Regarding research, the emphasis was mainly on Palaeontology, Anthropology and Archaeology. Dr Hoffman passed away unexpectedly while on a field trip in September 1969.

The third Director, Dr J.J. Oberholzer, was instrumental in increasing numbers of Museum staff, from 26 in 1970 to 130 in 1985. The increased number of scientists allowed the Director to devote all his time to management and administration. Conservation and research became the responsibility of specific research departments and several new departments were established. Most of the satellite museums (First Raadsaal and Wagon Museums, Freshford House Museum and the Florisbad Quaternary Research Station) were also established during this time. Oberholzer was also instrumental in negotiating for the acquisition of an art museum for Bloemfontein. Dr Oberholzer resigned in 1985 to become Chief Director of the Durban Museums.

Dr C.M. Engelbrecht was appointed Director in 1986. At this time, the shortage of accommodation - offices as well as storage space - became critical. A "temporary" office block (still utilised today!) was erected, and additional space was rented in a building near the Museum. The transformation of Oliewenhuis (at the time the Bloemfontein residence of the President of South Africa) into an art museum of international standards was undertaken. Due to changes in National Government structures, the question of the Museum continuing to be administered as a nationally funded institution (as opposed to at provincial level) was hotly debated. Dr Engelbrecht, together with the Council, successfully opposed the proposal for the Museum to be managed by the Free State Province. The Museum also entered the digital era, by digitising all databases of collection material. Dr Engelbrecht retired in 2003.