[1] The custom house is located at the site of the former main port of the city of San Juan, north of the former Spanish Arsenal of San Juan, and next to the Las Dársenas and Immigrants' Square (Plaza del Inmigrante) and the Jose V. Toledo Federal Building and United States Courthouse.

The large two-storey custom house is considered by the NRHP to be a superb example of Spanish Colonial Revival architecture in Puerto Rico and the Caribbean.

It was built between 1924 and 1931 at the site of a smaller 18th-century custom house, at a critical location that used to function as the central business district of San Juan during the late 18th and early 19th centuries, and the site of the main port of Puerto Rico (today the main cruise ship port section of Old San Juan) before the construction of the new port (Puerto Nuevo) located along the southern edge of the Bay of San Juan.

This was done as a territory-wide project to enlarge and upgrade the governmental properties in Puerto Rico during the early 20th century.

Construction was made by the Philadelphia-based Richmond and Kemp Ornamental Iron and Bronze and by the North American Wood Products Company of New York City.