The Custom House was commissioned by the Scottish Boards of Customs and Excise and constructed between 1810 and 1812. The chosen site, previously used for shipbuilding, was auspicious in that it was prominently visible from the sea and lay adjacent to the entrance of the new East Dock, which was completed in 1806. Once the West Dock was completed in 1817, they could hold a combined total of 150 ships, all of which had to pass immediately behind the Custom House when entering or leaving.
The building was designed by Robert Reid. The architecture was specifically intended to give the building a severe and commanding character, reminding people of the power of the government. Reid utilised the increasingly fashionable Greek Revival style, most obviously visible in the two large Doric columns on the façade. The original carved and painted Royal Arms, used by the monarch of the time King George III, have survived in the central pediment and indicate the governmental purpose for which the Custom House was built.
As the space needed by the Customs and Excise Office began to shrink, other organisations moved into the building. This included a Post Office in 1906 and the Mercantile Marine Office in the 1960s. Finally, in 1980, the decision was taken to sell the building. It was bought by the National Museum of Antiquities of Scotland (now part of the National Museum of Scotland). Despite plans to open up sections of the building for temporary exhibitions, it was used almost exclusively as storage space for the Museum’s reserve collections.