On 1941, Emile Boldoc of the Oblate Fathers (OMI) invited the Marist Brothers from the Province of United States to start an educational mission in Mindanao.

The school building was already built around 1945 but because of World War II, the planned opening was delayed for a couple of years.

The Religious of Virgin Mary (RVM) Sisters, who had been helping the Oblates in running the school, then took care of the girls' department (now Notre Dame – RVM College of Cotabato), while the Brothers has the boys' department, thus giving birth to Notre Dame of Cotabato (Boys' Department).

In June 1996, the school opened an afternoon shift program for boys and girls.

In June 2000, the school started to admit girls to the regular day shift session.