The Náprstek Museum Archives are not accredited. They are part of the collection department of the Náprstek Museum, methodically managed by the National Museum Archives. Approximately 200 linear metres of archive materials are stored here, originating mostly in the second half of the 19th century. The archives contain approximately 100 fonds and collections. The majority of them are personal fonds, meaning the written documents of various personages.

The key fonds concerns the founder of the museum, Vojta Náprstek, and his family. In addition, there are the personal fonds of our foremost travellers (Holub, Frič, and others), researchers, ethnographers (Pertold, Krása) and famous expatriates (opera singer Jarmila Novotná). In much smaller numbers, there are also other fonds, concerning, for example, various societies (the First Ladies' Boarding School in Prague, Household, the Ladies' American Club) and institutions (the Czechoslovak Foreign Institute).

Two large archive collections are also held here. First is the collection of Expatriatism, which contains materials documenting the lives of our expatriates; then there is the Scrapbook collection, which is a set of 320 scrapbooks. The archive material is largely unorganized. The overview of the material gives only the list of boxes and the card catalogue organized by name.

Since 2009 the material has been archived according to the methodology of the National Museum Archives. The archive tools are created in the Bach Inventář 2007 programme and selected archive materials are being digitalized. Since 2011, the archive fonds have been registered in the central register of the National Archival Heritage. In the same year, the archives were removed from the Náprstek Museum Library and included in the collections department of the Náprstek Museum.