In 1796, the Jews of St. Thomas founded this congregation. Only 9 Jewish families belonged to the congregation in1801, but by 1803 it had increased to 22, with arrivals from England, France, and the Caribbean islands of St. Eustatius and Curacao. In 1804 the small synagogue was destroyed by fire and replaced in 1812. The congregation grew so large that in 1823 it was dismantled and a larger one erected in the same location on Synagogue Hill.

The sand on the floor is most likely derived from a practice among crypto-jews during the Spanish Inquisition. During that time many were forced to convert to Christianity but secretly continued to practice Judaism. Those who were caught "backsliding" were tortured and burned at the stake. Consequently, crypto-jews gathered together in cellars for prayer and a sand floor helped muffle the sound of their prayers and songs.

A reception can be held for up to 10 people in the museum located adjacent to the synagogue.