The Customs House is built parallel to the straight breakwater that links the first and second piers of the port of Thessaloniki. From this prominent position it dominates the other harbor installations and stands at the heart of the historic center of the port.

Construction for the artificial harbor began at the end of the 19th century, as part of the attempt by the Ottoman authorities to turn Thessaloniki into a modern commercial city. The construction of the Customs House within a period of three years was undertaken by the engineer Eli Modiano, a Thessaloniki native Jew of Italian descent. The foundation stone was laid in August 1910 by the former Minister of Finance Tsavit Bey (Dohnme of Thessaloniki) and the building was completed by the end of 1912.