The Guggenheim Hermitage Museum is managed and operated by the Solomon R. Guggenheim Foundation. The two institutions are partners in an international alliance in which joint initiatives are undertaken and resources are shared to facilitate each institution's long-term goals. The Guggenheim Hermitage Museum is under the patronage of the Minister of Culture of the Russian Federation, Dr. Mikhail E. Shwydkoi.

The Guggenheim Hermitage Museum was conceived as a venue for the presentation of exhibitions based on the collections of the Guggenheim and Hermitage museums. All programming is generated by the directors and curatorial staffs of the Guggenheim and Hermitage museums. Exhibitions change approximately twice a year.