The Graduate School started as the graduate program of the Northern Luson teachers College (NLTC) in June 1963, offering Master of Education, major in administration and supervision. It gradually offered other major fields of study, namely: health education, English, Filipino, guidance and counseling, child study and development, and home economics. In June 1976, the NLTC became the Northern Luzon State College (NLSC) by virtue of PD 994. It was at this time that the Master of Arts in Public Administration was opened.

Presidential Decree 1279 merged the NLSC with the Mariano Marcos Memorial College of Science and Technology to establish the Mariano Marcos State University (MMSU). The NLSC campus then became MMSU’s College of Education (CE). The same presidential decree transferred the higher education courses of the Ilocos Norte College of Arts and Trades (INCAT); hence the Master of Arts in Trade and Vocational Education (MATVE) as a degree offering of INCAT was absorbed by the CE and became part of its graduate programs. The existing curricula were enriched and the Doctor of Education, major in educational management, was offered.

The Graduate School was finally established in 1981 and has since become an autonomous unit of the university. From then on, other graduate programs were introduced, namely: master of agriculture, master of science in agriculture, master of science in agroforestry, master of rural development, master of science in rural development, master of nursing, master of arts in nursing, doctor of philosophy in rural development, and doctor of philosophy in crop production management.