After the Spanish-American War when Puerto Rico became a territory of the United States, English-speaking immigrants including missionaries from the United States, began to settle on the predominatly Roman Catholic island.  Shortly thereafter, the Methodist and Presbyterian churches both started congregations in Puerto Rico, the Methodists in Santurce in 1900 soon followed by the Presbyterians in Old San Juan.

The design of Our Lady of Lourdes Chapel was commissioned in 1907 to Nechodoma by the Methodist Church for whom he did several other designs as well.  For this chapel, Nechodoma used the English Neo-Gothic Revival Style instead of his traditional Prairie Style.  According to Thomas Marvel, this is a purely traditional design with nothing original to it and reflects none of the spirit of some of Nechodoma's early work.   

Certain traits of this design closely resemble St John's Cathedral on Market Street in Jacksonville, FL designed for the Episcopal Church by the Columbia, SC firm Wilson & Edwards.  It is worthwhile noting that Nechodoma lived and worked near St. John's Cathedral in Jacksonville before relocating to the Caribbean.  

The Gargoyles and battlements on the tower that can be appreciated on this Wikimedia Commons Image, the stained glass window and the rose window above it as well as the Celtic Cross on the main façade are all characteristics that can be seen both at St. John's Cathedral as well as at Our Lady of Lourdes.

In 1917 the interdenominational Union Church of San Juan was established by protestant, English-speaking parishioners of both the Methodist and Presbyterian congregations.  At that time Our Lady of Lourdes Chapel was leased and later acquired by the Union Church of San Juan.  In 1956 the Union Church of San Juan sold the property for $70,000.  Its new owners gifted it to the Catholic Church in 1959.

It was included in the National Register of Historic Places in 1984.