The museum in Kostroma was founded in 1891 thanks to the Kostroma Provincial Scientific Archive Commission. In 1913, the commission moved to the building of the Romanov Museum, constructed for the 300th anniversary of the House of Romanov by the city architect. This building, located at the beginning of the current Mira Avenue, was ceremoniously opened in the presence of the imperial family. The museum's initial collections were related to the history of the Romanov dynasty.

Since 1913, the museum has undergone numerous reorganizations. Throughout the 20th century, its collections were enriched with unique exhibits, such as the artistic and graphic works of E. V. Chestnyakov, the weapons collection of the noble Cherevins, and the Eastern collection of G. A. Ladyzhensky.

In 1958, the Kostroma State Historical-Architectural and Art Museum-Reserve was established at the Ipatiev Monastery. Restoration work allowed for the recovery of ancient structures, freeing them from later alterations.

In 1993, despite protests, the territory of the New City was transferred to the monastic community. In 2004, the entire monastery complex was handed over to the Russian Orthodox Church, which caused a scandal, and the collections of the museum-reserve had to be urgently placed in various unsuitable premises.

In August 2005, a reorganization took place, resulting in the merger of two major museums of the city and region: the Kostroma State United Art Museum and the Kostroma State United Historical-Architectural Museum-Reserve 'Ipatiev Monastery.'