The building that houses the Thessaloniki Branch is located in the wider area of the Ares Field camp, where today the Headquarters of the 3rd Army Corps is located. The building was designed by the Italian architect Vitaliano Poselli (1838-1918) at the beginning of the 20th century and was originally used by the Ottoman Army.

When Thessaloniki was liberated by the Greek Army in 1912, it became its property and military units were installed in it. After a period of disuse, the local political and military leadership decided to house the city's War Museum here as a branch of the Thessaloniki War Museum.

Renovation and reconstruction work began in 1993. After the completion of the works, the museum opened its doors to the public in 2000.