The seminary was founded by then Archbishop of Manila Rufino Cardinal Santos. In 1953, Cardinal Santos decided to put up an Archdiocesan High School Seminary to accommodate a large number of boys with initial signs of priestly vocation. OLGMS, a subordinate portion of San Carlos Seminary first became known as San Carlos Minor Seminary and was put under the care of the CICM fathers. It is located on a four hectare of prime land overlooking Pasig River, covering the war-ravaged Guadalupe Shrine and Augustinian Seminary.