In June of 1961 in El Paso, Texas and on the Feast of Corpus Christi, Bishop Sidney Matthew Metzger (July 11, 1902 – April 12, 1986) blessed the land for the new minor seminary and placed in under the patronage of St. Charles Borromeo (1538-1584) a Cardinal Archbishop of the Archdiocese of Milan, Italy and who was responsible for significant reforms in the Catholic Church including seminaries for the education of priests. At least one other seminary in the United States in Overbrook/Wynnewood, Pennsylvania is dedicated to St. Charles Borromeo.
The Very Reverend R. A. Vonder Haar was named as the first rector of the newly formed seminary and classes were conducted in Jesuit Hall. Students lived at home while construction proceeded on the main campus. In July 1963 His Excellency appointed the Very Reverend James B. Hay as the second rector and over the next three years classes were gradually transferred from Jesuit Hall to the Seminary, which was considered part of the local diocese school system and accredited by the Texas Education Agency.
In the fall of 1974 Father John Peters was named the third rector. Two army barracks purchased a year prior were strengthened with cinder blocks and re-roofed. Father John Peters is currently serving as Pastor of Sacred Heart Catholic Church in Hallettsville, Texas.
In 1978 Patrick Flores was named Bishop of El Paso and Father Stephen Peters was named the fourth rector of St. Charles Borromeo Seminary. However within months Bishop Flores was elevated to serve as Archbishop of the largest diocese in the United States in San Antonio, Texas. Father Stephen Peters currently serves as Adjutant Vicar of the Tribunal Office for the Diocese of El Paso.
In 1980 Bishop Raymond Pena was named Bishop of El Paso, Texas, and Rev. David Fierro was named rector of St. Charles Seminary. The High School Seminary was closed and all resources dedicated to college level seminary formation. Msgr. David Fierro currently serves as Pastor of St. Matthew Parish in El Paso, Texas and as Defender of the Bond for the Tribunal Office of the Diocese of El Paso, Texas.
From 1985 to 1999 Father Jose Sanz, D.L.P. was named Rector. The Diocese of Casa Grande Mexico and the Diocese of Brownsville, Texas sent their seminarians to St. Charles. Father Jose Sanz, D.L.P currently serves as Director of Serra House of formation.
In April of 1995 Armando X. Ochoa was named Bishop of the Diocese of El Paso, Texas and in October of 1999 Father John Telles was named the Rector of St. Charles. The seminary received students newly arrived from Morelia Mexico via the Diocese of Atlanta. In 2010, Father Miguel Angel Sanchez was named Rector of St. Charles Seminary.
In May, 2013 His Excellency Mark J. Seitz was named the 6th Bishop of El Paso, and in July 2015, Father Mariano Lopez was named the Rector of St. Charles. Since its founding in 1961 over thirty priests have received either or both their High School and College Formation at St. Charles Seminary.