The National Museum is located in three different places in central Windhoek.

It is located on Lüderitz Street and shares a building with the Windhoek Public Library.

It is located at the Alte Feste (English: Old Fortress) building on Robert Mugabe Avenue, next to the Independence Memorial Museum.

The administrative offices of the National Museum and the National Museum Library, established in 1963, are also located on Robert Mugabe Avenue, opposite the Alte Feste.

[2] It is planned to repurpose the building into a centre of arts, craft, and heritage.