One section of the Archaeological Museum is formed by the Egyptian collections, the most important in Italy after those of Turin.
The original core of the Egyptian section, which was formerly housed in the Cenacolo di Foligno, was the Nizzoli collection, purchased in 1824, together with pieces from the Italian expedition headed by Ippolito Rosellini, which took place at the same time as the French expedition of Champollion.
The collection was subsequently added to through numerous acquisitions and donations, as well as by the finds of the 1885 and 1891-92 archaeological campaigns in Egypt led by Schiaparelli.

The museum's most famous work, the bronze Greek statue known as the Idolino, is housed in the Room of the Idolino.
Displayed in the Bronze Gallery are three large Etruscan bronzes: the statue of Minerva, the famous Wounded Chimera of Bellerophon, from the 5th century BC, and the Harranguer, a monumental funerary statue from the 3rd century.
The section dedicated to Attic black-figure vases houses the famous François Vase, from the 6th century BC, attributed to the Greek artist Cleitias.