Founded in 1865 by the Oblates of Mary Immaculate, Saint Joseph Academy opened and closed several times in its earliest years. In 1906, Marist Brothers from Mexico arrived and assumed operation of the school. It initially operated as an elementary school for boys. By 1916, the Academy accepted boarders and in 1926, the three-story building, known as the “Old Saint Joseph Academy”, was constructed on a site where the International Bank of Commerce now stands in downtown Brownsville. In 1930, the first high school students were graduated. In 1940 the Sisters of the Holy Ghost assumed operation of the elementary school. The new campus on its present location was opened in 1959, and served boys in grades 7 - 12.
In 1971, the school became coeducational, accepting its first female students in grades 7, 8 and 9. From the late nineteen-seventies until present, the school has undergone a gradual process of growth and transformation evident in the expansion of its student body and the improvement of its programs and facilities. In August 2005, the Academy opened the new Middle Division Building, designed to meet the educational and developmental needs of its middle division students.