The Mimara Museum is located in the remarkable architectural "Lower Town high schools complex", which was built at the end of the 19th century in the spirit of historicism: it is a very valuable example of the neo-Renaissance palace, and is the work of two German architects from Leipzig/Berlin, A. Ludwig & L. Th. Hülssner, who were specialists in the design of school buildings. The plan was commissioned in 1892, and the construction work was opened to the public in 1895, in the occasion of the king and emperor Francis Joseph I, who came that year in Zagreb.

The historical credit for the construction of the complex must go to the art historian, painter and politician Izidor Kršnjavi (Našice, 1845 - Zagreb, 1927), who from 1891 to 1896 was Head of the Religion and Teaching Department (the equivalent to minister of education). Kršnjavi was the initiator of many cultural and educational programmes and built many of the fundamental institutions of Croatian culture, science and education.

Kršnjavi's original architectural and educational programme for the gymnasium complex in Roosevelt Square incorporated the humanist concept of joining a series of school and museum institutions around a forum.

However, he had to give up this conception, so complex in both substance and symbolism, and in its actual accomplishment, Izidor Kršnjavi's "School Forum" was reduced to the rather simplified high school complex.
In its position and in the elaborated layout of the ground plan, in its articulated façades and in the solemn views, this complex has both architectural and urbanistic values and a great part to play in giving shape and meaning to the appearance of the Lower Town of Zagreb. As a protected cultural asset, the building entered in the Ministry of Culture's register of immovable monuments of culture.

The Mimara Museum is situated in the central part of this architectural complex which had until that time housed the 1st and 4th high schools. Today the 5th High School (“gymnasium”) is in the northern wing, while the "Izidor Kršnjavi" Elementary School occupies the southern wing, sharing it with the First Private Art High School.