The ancient and valuable items held by the museum are systematically organized into several collections. The Prehistoric, Classical (Greek and Roman), and Mediaeval Collections follow the usual chronological system of all European museum departments. The museum also contains an Egyptian Collection, the only one in this region, as well as a Numismatic Collection that is one of the largest in Europe and beyond. As a whole, most of the material is of local provenience, from regions historically belonging to Croatia, although the Archaeological Museum in Zagreb, in contrast to similar museums in Croatia, also contains rich collections and individual monuments of foreign origin. Along with the already mentioned Egyptian Collection and a large segment of the Numismatic Collection, several important collections of Greek and Roman artifacts come from foreign lands. These include an important collection of Grecian painted vases from southern Italy and Greece, a valuable collection of stone monuments of Italic provenience - sculptures, reliefs, inscriptions, etc. - formerly in the possession of Count Laval Nugent, and in particular the famed wrapping of the Zagreb mummy, the Etruscan "linen book" of Zagreb (Liber linteus Zagrabiensis).

In addition to the various departments dealing directly with the archaeological collections, the Archaeological Museum contains one of the most extensive archaeological libraries in Croatia. The conservation laboratory should also be mentioned, capable for the most part of protecting and preserving the specific types of archaeological material held by the museum, as well as aiding similar institutions as much as possible.