National Historical Museums is led by a Director General, who is also Director of the Swedish History Museum. The Director General is appointed by the Government for a period of six years. The Royal Coin Cabinet has its own director, who is appointed by the agency. The figure above shows how the agency is organised.

The agency has had an Advisory Council in place since 2015. The council comprises: Anders Högberg, associate professor and lecturer at the School of Cultural Sciences, Linnaeus University; Eskil Franck, associate professor of theology and former director of the Living History Forum; Johanna Sandahl, agronomist and chair of the Swedish Society for Nature Conservation and Seher Yilmaz, communications consultant and chair of Equalisters.