Among the three American-era customs houses in the Philippines, it is the second largest (after Manila's) and second oldest (after Cebu's, now known as Malacañang sa Sugbo).

Planning for the new custom house of the port of Iloilo started in 1913, with Consulting Architect William E. Parsons initially overseeing the project.

2 of the Bureau of Public Works Bulletin (July 1915) described the circumstances leading to its construction:[5] Ralph Harrington Doane replaced Fenhagen as Consulting Architect in 1916, and prepared the final architectural plans of the building.

Doane was very critical of Parsons' work in the islands, and endeavored to improve the aesthetics i.e. ornamentation of public buildings.

The Manila Customs House, designed by Juan Arellano and constructed towards the end of the American colonial period, is a more ornate version.