The museum began in 1883 as a simple collection of antiquities; it was about the time when the Minoan civilization was beginning to be rediscovered, and shortly before the first excavations using proper scientific methods.

It was also during the period when Crete was a virtually autonomous part of the Ottoman Empire, after the Pact of Halepa of 1878, later followed by the independent Cretan State (1898-1913), protected by a military occupation by the Great Powers.

The director of the Heraklion Museum was then Spyridon Marinatos, who made great efforts to find funds and persuade the locals and the central government alike that a new solid building was needed.

In 1935, Marinatos succeeded in engaging Patroklos Karantinos to build a sturdy structure that has withstood both natural disasters and the bombing that accompanied the German invasion in 1941.

Karantinos applied the principles of modern architecture to the specific needs of a museum by providing good lighting from the skylights above and along the top of the walls, and facilitating the easy flow of large groups of people.

The two-storeyed building has large exhibition spaces, laboratories, a drawing room, a library, offices and a special department, the so-called Scientific Collection, where numerous finds are stored and studied.

[3] The Heraklion Archaeological Museum is a Special Regional Service of the Ministry of Culture and its purpose is to acquire, safeguard, conserve, record, study, publish, display and promote Cretan artefacts from the Prehistoric to the Late Roman periods.