The Museum of the City of Rijeka is mentioned in city history as early as 1875, when Gov. Francis Joseph donated a glass to Rijeka residents in an effort to preserve it as an exhibit of his own City Museum. the Museo Civico City Museum was finally opened in 1893 and the Sušak City Museum was opened in 1933.

As a modern institution, the Museum of the City of Rijeka has its origins in the Museum of the People's Revolution of Rijeka, founded by decision of the City People's Committee of the Susak Municipality on May 30, 1961. The headquarters of the Museum of the People's Revolution was in the former home of Count Laval Nugent, next to Trsat Castle, in Petr Zrinski Street. Due to inadequate conditions, it was moved on November 12, 1976 to a new, modern, purpose-built building, with a permanent exhibit, organized collections and adequate museum standards.

It operated as an institution until April 11, 1994, when by the decision of the City Council the Museum of the National Revolution was renamed the Museum of the City of Rijeka. The new establishment continued to operate in the same building, located in the city center, in Governor's Palace Park. The building is a modernist object designed by the architect Neven Šegvić in 1976 for the museum. For this project, architect Neven Segvic received the Republican and Federal Award for the Best Architectural Achievement in Croatia in 1976. In addition to the building, the City Museum inherited its predecessor's documentary material, storing it in newly formed collections.