In 1884, the Third Plenary Council of Baltimore decreed that every parish must have a Catholic school. Following that decree, Bishop A.J. Schuler of the El Paso Diocese authorized Fr. Doherty, Pastor of St. Joseph's Church, to begin construction of a school in 1923. The architectural firm chosen was Trost and Trost. Fr. Doherty engaged the services of the Sisters of Loretto to administer and staff the school. They began with four grades and every year thereafter another was added. 

In 1938 Fr. P.A. Ryan, successor to Fr. Doherty, obtained permission from Bishop A.J. Schuler to add a parish church and rectory to the existing school on Hueco Street. This building was also designed by Trost and Trost Architects and is crowned with an impressive 70-foot tower named after the benefactors-The Momsen Family.

The Sisters of Loretto administered the school until 1977, and then it became the responsibility of the laity. In 1989, Fr. Francisco Herrera, Pastor of St. Joseph's Church, invited the Brothers of the Poor of St. Francis, who were in Arkansas, to assume administration of the school until 2015. Today it is successfully administered by laity.

During the past twenty years, a number of renovations on campus have been completed which enhance the old charm of the buildings with the grace of a modern appearance. St. Joseph's School is accredited and consists of grades Pre-K through Eighth and has an enrollment of about 300 students and a faculty of about 40.