The collections of the National Museum in Krakow number almost 780 000 objects. Of these over 300 000 belong to the collection of the Princes Czartoryski Museum and Library which is managed by the National Museum in Krakow. There are artefacts from every period of history. The oldest exhibits in the Museum date from prehistoric times, though these are limited in number as the Museum does not usually collect archaeological artefacts, with the exception of classical archaeology. The Museum also possesses a separate collection of ancient art, recent works acquired from contemporary artists, and collections of medieval and modern art from the 19th and 20th centuries.

The core of the collection is Polish art (painting, sculpture, drawing, decorative art), though there are also numerous western European works, a collection of religious art related to the Orthodox Church, and an extremely valuable collection of oriental art, mainly from Japan. Besides works of art the Museum also collects library collections (including old prints, manuscripts and cartography), numismatics and historical photographs. A particularly interesting department is the Studio of the Iconography of Krakow with its collection of historical views and photographs of the city.

Most of the Museum's collections were acquired through donations, mainly during the period of partitions and the twenty-year interwar period. Major donations were made by Feliks Jasienski, Count Emeryk Hutten-Czapski, Erazm Baracz, Stanislaw Ursyn-Rusiecki, Wiktor Wittyg, Edward Goldstein, Helena Budzynowska née Dabczanska, Stanislaw August Poniatowski and many others.

The Museum's collections are divided among twenty-one departments, each of which collects items of a particular type (e.g. the Numismatics Room). The collections are made available to the public in permanent and temporary exhibitions. Artefacts which are usually kept in the Museum's stores are also made available for research purposes.