Excavations at ancient Abdera began in 1950. The finds were initially housed at the Archaeological Museum of Kavala. From 1973 onwards, when the Prefecture of Xanthi was incorporated into the 19th Ephorate of Prehistoric and Classical Antiquities of Komotini, the finds were kept at the Archaeological Museum of Komotini.
In 1976, the Ministry of Culture initiated procedures for the construction of a museum in Abdera. The decision to establish the museum was signed in 1984. In 1985, the Community of Abdera granted a plot of land within the village for this purpose. Construction work began in 1989 and was completed in 1992. The building was officially handed over in 1993. Preparatory work for the exhibition began in 1994.
Between 1995 and 1998, the archaeological finds selected for display were transferred from the Archaeological Museums of Kavala and Komotini. In 1997, the Central Archaeological Council approved the Ephorate’s proposal for the exhibition programme. The re-exhibition works were carried out in 1998-1999. The Museum was officially inaugurated on 20th January 2000.