The pentagonal building opposite the main gate of the Fortetsa has been accommodating the Archaeological Museum of Rethymnon since 1991. Originally constructed by the Turks as an effort to strengthen the city’s defense, the building has undergone significant alterations due to its different functions over the centuries, including serving as the civic prison until the 1960s. The first collection began in 1888.

The museum displays discoveries from various areas of the prefecture, spanning from the Neolithic to the Roman era.

Some of the most notable exhibits of the museum include a clay larnax decorated with a hunting scene, a figurine of the Minoan goddess, a marble statue of Aphrodite, a marble violin-shaped figurine, a clay model of a shrine, a stone model of an offering table, a pyxis strainer from Stavromenos, a head of a terracotta female figurine, a part of a marble funerary stele, and a part of a marble funerary stele.