The history of museology in Pula precedes the 1902 founding of Pula's civic museum. Before the first museum institution in Pula was created early in the 20th century the stone monuments that lay unprotected throughout the city and its immediate surroundings were collected for safekeeping at the Temple of Augustus in the Forum.

The discovery of numerous stone, ceramic, and metal objects in nearby Nesactium in the course of investigation performed in 1900 and 1901 by the Società Istriana di Archeologia e Storia Patria (Istrian Archaeology and Homeland History Society), was the basis for the establishment of the Museo d'antichità (Museum of Antiquities) and the Museo Civico della Città di Pola (Pula Civic Museum) in 1902. The museum was housed in a building that no longer exists on the Uspon svetog Stjepana alley not far from the Arch of the Sergii.

A merger of the national civic collection (of stone sculpture) and the provincial museum in Poreč (Museo Provinciale) in 1925 created an institution of regional stature, the Regio Museo dell'Istria (Royal Museum of Istria). The scope of the collections necessitated new premises and the former building of the German-language State Gymnasium on the eastern slope of the Kaštel hill in the city core, built in 1890, was repurposed to house the museum, which opened to the public in 1930. The institution was renamed the Archaeological Museum of Istria in 1947 and has continuously operated from this building to this day.

Most of the artefacts were removed to Italy under the Anglo-American administration of the immediate post-World War II period. Systematic work and a sustained effort were invested in the development of an overall museum collection concept, including the restitution of a part of the archaeological material from Italy in 1961. Adapted space for the collection of stone sculpture was opened in the ground-floor rooms and corridors of the museum in 1968, and in 1973 halls of the building were developed to house prehistoric, classical antiquity, late antiquity, and medieval period exhibitions. Work on the remodelling and extension of the main museum building were launched in 2013 and completed in 2021. A new AMI permanent exhibition is now being developed.