Accounts of the flagellant roots of the Brotherhood date back at least a thousand years to the flagellant orders in Spain and Italy. Flagellation in the Christian context refers to the Flagellation of Christ, an episode in the Passion of Christ prior to Jesus' crucifixion. The practice of mortification of the flesh for religious purposes was utilized by some Christians throughout most of Christian history, especially in Catholic monasteries and convents.
In the 13th century, a group of Roman Catholics, known as the Flagellants, took this practice to its obvious ends. The Flagellants were later condemned by the Roman Catholic Church as a cult in the 14th century because the established church had no other control over the practice other than excommunication.
The current incarnation of flagellants resides within the Brotherhood and its history dating to the early 19th century. Following Mexican independence from Spain in 1821, Church authorities in Mexico withdrew the Franciscan, Dominican and Jesuit missionaries from its provinces, replacing them with secular priests. They failed, however, to replace the missionaries with an equal number of priests, depriving many secluded communities of a resident clergyman. Accordingly, many of those small communities could expect only a once-yearly visit from a parish priest.
The men in those communities eventually came together in the absence of a priest and dedicated themselves to the purpose of providing mutual aid, community charity and to memorialize the spirit of the penance and the Passion of Christ. They gathered in meeting houses known as moradas. Los Penitentes were perhaps best known for their songs of worship, called alabados, and for their ascetic practices, which included self-flagellation in private ceremonies during Lent, and processions during Holy Week which ended with the reenactment of Christ’s crucifixion on Good Friday.
Archbishop Jean Baptiste Lamy and his successor, Jean Baptiste Salpointe, unsuccessfully attempted to suppress the brotherhood in the latter part of the 19th century as a part of the "Americanization" of the Church in New Mexico, driving its membership underground. For this reason, Los Penitentes are sometimes described as a “secret society”.
The modern embodiment of the Brotherhood began in the middle of the 20th century with the reconciliation between the Brotherhood and the Church. In June 1946, Miguel Archibeque began his first term as the Brotherhood's first Hermano Supremo Arzobispal (Archiepiscopal Supreme Brother). His first term lasted 7 years and it was during this term in January 1947 that the Brotherhood was officially recognized and sanctioned as an organization by Archbishop Edwin V. Byrne. By this time, membership had declined markedly since the turn of the century, but the Brotherhood continued to perform a modified form of religious rituals and to pursue its commitment to acts of community charity. In June 1953, Miguel Archibeque was replaced by Roman Aranda of Las Vegas, New Mexico. Aranda served for one year and was replaced by Archibeque in June 1954. Archibeque served the Brotherhood until 1960 when he was replaced by the third Hermano Supremo Arzobispal, M. Santos Melendez, of Mora, New Mexico, who continues to serve in this capacity.