The museum is operated by the Neanderthal Museum Foundation. It cultivates the cultural heritage "Neanderthal" for the general public as well as for specialist research. 

Initially, the foundation has been supported by the District of Mettmann and the Neanderthal Museum Association. The museum is only partly run by public funds. Most of the museum's fund is carried by entrance fees and proceeds from sales. 

In 1996, the construction and arrangement of the museum was supported by NRW-Stiftung Natur, Heimat and Kultur and RWE. Since 2002, new supporters joined: Kreissparkasse Düsseldorf, the Rhineland Regional Council (LVR), as well as the cities of Erkrath and Mettmann.