Joya de Cerén was discovered in 1976, when a tractor was removing dirt to build silos that would be used to store grains. While removing dirt from a hill, the tractor discovered part of a house. Fortunately, Dr. Payson Sheets of the University of Colorado investigated this house shortly thereafter and determined that it was at least 1,400 years old, and has since been protected and studied. The park was created on June 19, 1993, and the current building was inaugurated on December 12, 2003.

Declared by UNESCO a World Heritage Site in 1993, Joya de Cerén provides insight into the daily life of a Mayan farming village from 1,400 years ago (7th century), and is the only one known in El Salvador. The site consisted of a small farm that was buried by five meters of volcanic ash during the eruption of the Caldera Lagoon, for what has been called the New Pompeii, and the Pompeii of the Americas. Its state of conservation is unbelievable.