In 1957-1962, Fr. Sean Nolan of the Missionary Society of Saint Columban (MSSC) laid the foundations of Saint Columban College, then known as Saint Columban School in Pagadian City. He built the high school building, a wooden structure made possible through the help of Fr. Nolan's family and friends in Ireland. As the first director of the school, he opened the first and second year levels with Sr. Isabel of the Angels Narciso, SPC, as the first principal. Sr. Isabel is remembered for her composition of the SCC graduation song and for starting the school publication, The Harp.
The years that followed saw a succession of principals who were Sisters of St. Paul de Chartres. In 1962-1965, it was Sr. Marie Andre Madrid; 1965-1966, Sr. Marie Anselme; 1966-1967, Sr. Mary Agnes Pawig; 1967-1969, Sr. Saint Jean; 1969-1971, Sr. Mary Norbert; 1971-1972, Sr. Mary Imelda; 1972-1973, Sr. Carmina de Jesus Laungco; 1973-1976, Sr. Milagros Amos; 1977-1981, Sr. Marie Anstasie de Jesus Dongallo who started the construction of the 2-room (2-storey building) high school building; 1982-1992, Sr. Mary Gabriel Prado who was responsible for the completion of the 8-room high school building, now a storey building. She also built the high school chapel dedicated to Our Lady of Lourdes through the donation from friends in Germany. In 1993-1995, Sr. Felicitas Bernardo served as the last SPC principal of Saint Columban High School. During her 3-year, Sr. Felicitas introduced additional subjects in the curriculum with Accounting subjects for 3rd and 4th, and Stenography and Typing for the 1st and 2nd year students.
In 1995-1998, Mr. Ramil Ecot took the leadership. The revision of the high school curriculum was done, and upon approval of the Administrative team, it was immediately implemented. SCCHS had a 100% passing rate in the National Achievement Scholastic Aptitude Test (NSAT). In 1999-2000, Mrs. Theresa Moron was the principal. The same curriculum was continued while the high school was under the supervision of the Diocesan Schools Superintendent.
From 2001 to date, Mr. Gilbert A. Celesio is the Principal. In June of 2006, the High School Department, together with the Diocesan schools, adopted the Dynamic Learning System. The essential components of the program are Parallel learning groups, Activity-based multi-domain learning, In-school comprehensive student portfolio, Strategic study-rest periods, and Strengthened spiritual and aesthetic formation. The system is patterned after the Barnido model which was introduced in Jagna, Bohol. Mr. Celesio is responsible for the construction of the students' kiosk, a project of the Alumni batch '71. The High School grading system and finance system were introduced in the school year 2007-2008.