The history of museology in Pula is older than the founding of the City Museum of Pula in 1902. The establishment of the first museum institution in Pula in the early years of the 20th century was preceded by the collection of stone monuments that lay unprotected throughout the city and its immediate surroundings, and their placement in the Temple of Augustus in the Forum.

The discovery of numerous stone, ceramic, and metal objects in nearby Nezakcij, during research conducted in 1900 and 1901 by the Istrian Society for Archaeology and Homeland History (Società Istriana di Archeologia e Storia Patria), was the basis for the establishment of the Museum of Antiquities (Museo d'antichità), or the City Museum of Pula (Museo Civico della Città di Pola) in 1902. Its headquarters were in a building that no longer exists today, on St. Stephen's Rise, not far from the Arch of the Sergii.

By merging with the National City Collection (stone monuments) and the Poreč Provincial Museum (Museo Provinciale), in 1925 it grew into an institution of provincial significance under the name Royal Museum of Istria (Regio Museo dell'Istria). The richness of the collections necessitated new space, so the former building of the State German Gymnasium on the eastern slope of the central city hill Kaštel, built in 1890, was adapted to the new needs of this museum, which opened to the public in 1930.  In 1947, the institution changed its name to the Archaeological Museum of Istria and has continuously operated from the same headquarters to this day.

After World War II, during the Anglo-American administration, most of the artifacts were transferred to Italy. Through systematic work and great efforts, after the restitution of a part of the archaeological material from Italy in 1961, a concept for the entire museum collection was developed. In 1968, the renovated lapidarium was opened in the ground-floor rooms and corridors of the museum, and in 1973, exhibition halls for prehistory, as well as ancient, late antique, and medieval exhibitions, were opened. In 2013, the adaptation and extension of the main museum building began, which was completed in 2021.  A new permanent exhibition of the museum is currently being prepared.