The first core of the Archaeological City Museum, a place where it would be possible to host both the Palagi collection of classical finds (among which the Roman Age copy of the Lemnia Athena by Phidias was included) and the attires coming from the Certosa excavations led by the archaeologist A. Zannoni from 1869 to 1873, was inaugurated on October 2nd, 1871, on the occasion of the V International Archaeology and Anthropology Congress in the presence of Prince Umberto I of Savoia. However, since 1714 the Royal University Antiquity Museum already existed: it was created by Luigi Ferdinando Marsili and was endowed with a large number of finds, but owing to the continuous growth of the archaeological collections it was decided to place the Museum in its current premises, that is, in the ancient St. Mary of Death Hospital (a 15th century building) that is anyway very well set in the architectural continuity of the Archiginnasio Palace. The building hosting the Museum was planned in its present shape in 1565 by the Bolognese architect Antonio Morandi, called "Terribilia" who added the portico that can be seen today.

The Archaeological City Museum contains a sector of its collection that is entirely dedicated to the history of the city from the prehistoric era to the Roman and late-ancient ages, besides a renewed Egyptian collection (one of the most important in Europe) that, in addition to the Greek-Roman and Etruscan one sets the Museum among the most remarkable ones in Italy. In particular, the Egyptian collection comes from the Palagi donation and boasts valuable pieces such as the Horemheb Relieves. Among the most interesting finds we must mention the head of Lemnia Athena, marble copy of the Roman Imperial Age from Phidias' bronze original, the statue attributed to Emperor Nero (exhibited in the Entrance Hall) and the rich funeral attires of Etruscan tombs. In the courtyard, a series of milestones from Via Emilia are kept together with a large number of tombstones coming from the so-called "Reno Wall" and tombstones coming from the ancient Jewish Cemetery of Via Orfeo. Some sections of remarkable importance and interest, also because of their recent rearrangement and the new museum layout are the Gypsotheque, made up of plaster copies of famous Greek and Roman sculptures and the informatics section, a new space reserved for the public, duly set up and equipped with five computers that will allow the visitors to access scientific and didactic programs developed over the last few years by the Museum staff with the help of computer technology. The coin and medal collection is extremely rich and precious. It was originally made up by two large collections which were then united: the University and the Palagi Collections, that together formed a core of about 10,000 pieces and that contain Byzantine, Mediaeval, Renaissance and Modern Age pieces (both Italian and foreign) as well as Greek and Roman ones. The Museum Library collects specialized books and magazines dealing with archaeological, numismatics, conservation and restoration themes.

After being closed for it's restyling, the Etruscan and Italic collection at the Archaeological museum is now open to the public completely re-arranged, with a new system of information and educational tools for children – consists of archaeological materials related to the Etruscans and other tribes who inhabited the peninsula between the early Iron Age (9th century BC) and the Roman domination.
These relics come from the city's oldest collections (including those constituted in the seventeenth century thanks to the heritage of Cospi, Marsili, Palagi), but also from the exchanges of materials that museums - up to the beginning of the last century – used to have in order to provide the public with comparisons between the local archaeological culture and that of other centers.