Initially, an independent part of the Thessaloniki International Film Festival, the Museum became autonomous in 2003 and operated for a period of time as a Public Legal Entity under the supervision of the Greek Ministry of Culture. In December 2010 it was integrated to the Thessaloniki International Film Festival.
Since April 2016 Élise Jalladeau is the Director of both the Thessaloniki International Festival and the Thessaloniki Cinema Museum.
A. Dermetzoglou was the first Director of the Thessaloniki Cinema Museum. He remained in post up until 2002 together with A. Papagiannopoulos who was appointed Chairman of the Museum's Board. Those were succeeded by G. Katsagelos and T. Psarras respectively. From 1-6-2005 up until the Museum's integration to the Thessaloniki International Festival in December 2010, Director was B. Kehagias and Chairman G. Mylonas. From May 2010 up until March 2016 Dimitris Eipides was the Director of both the Thessaloniki International Festival and the Thessaloniki Cinema Museum.