In 1948, NASIPIT was still a part of the Parish of Buenavista, whose Parish Priest was the late Fr. Martin Westeinde, a Dutch MSC. As the town progressed, population also increased and business gained momentum with the start of the logging industry of the Nasipit Lumber Company (NALCO). Fr. Martin and his co-adjurer Fr. Atanacio de Castro saw the need of putting-up a secondary school. Fr. De Castro was made in charge of the school.

It started its operation on July 1, 1948, with Rev. Fr. Francisco Van Dyke as the first Director. He was succeeded by Rev. Fr. Enrique Van Ma-anen, Rev. Fr. Vicente Portillo, Rev. Fr. Mateo Van Santvoord, and Rev. Fr. Anthony Krol in the order of succession. Rev. Fr. Krol was the last Dutch priest who served as the school director.

The school site is beside the rectory with an area of 1,630 sq.m. Fr. Gerard Cruisjen, one of the subsequent Directors converted the nipa-wooden structure into a concrete two-storey building with 16 classrooms.

When the Filipinization Law was implemented in 1975 a layman (now deceased) Mr. Gregorio Orias, became the first layman School Director until he retired in 1977. He was followed by Mr. Antonio L. Suarez, the first layman Director/Principal of the school. Faro Gatchalian followed until 1985 then Mrs. Necita Lim took the helm of the Directorship until 1991 while acting also as the Principal of St. James High School of Buenavista, an adjacent town of Nasipit . In 1991, Fr. Achilles Ayaton became the School Director until 1993. In 1994, Msgr. Cesar L. Gatela took over the School's Directorship until 1999 when he succumbed to a cardiac arrest in Cebu City. In his term, he opened the Pre-School Department with Sister Minah B. Hijada as the Administrator and he bought 19 computers integrating the Computer Technology subject to all levels of the High School Department.

The Teatro, Sayaw, at Awit Production (TESAW Production) Center of the Michaelinian Performing Arts was established on June 01, 1997 with Dr. Dennis P. Mausisa as the Founder and Artistic Director.

In 1999, after the sudden death of Msgr. Gatela, Msgr. Juan de Dios Pueblos, the bishop of Butuan appointed Msgr. Bienvenido A. Betaizar as the School Director who was later on promoted as School President until at present.

June 2000, Msgr. Betaizar opened the Grade School department with Mrs. Minda R. Cocon as the first Principal offering Grades I-IV and the College Department with Technical Courses offering with Mr. Antonio L. Suarez as the College Administrator until his death on February 2002.

June 2001, Baccalaureate Programs were opened which include Bachelor of Elementary Education, Bachelor of Secondary Education major in English, Bachelor of Science in Business Administration major in Financial Management and Bachelor of Arts in English Language. The Planning and Development Center was established with Dr. Dennis P. Mausisa as the Head of Office.

February 16, 2002, the name Saint Michael's Institute was replaced with Saint Michael College of Caraga as suggested by Mrs. Vanica P. Del Rosario during the 1st SMI General Assembly. The name was duly approved by the Securities and Exchange Commission.

In 2002, Dr. Dennis P. Mausisa unveiled the SMCC's Vision 2020 with the flagship program "Magbayanihan Tayo". SMCC's Vision 2020 is a long range master plan of SMCC for seven key areas: Personnel, Instruction and Curriculum, Physical Plant and Facilities, Library, Student Services, Community Extension Service, and Research and Accreditation. This year also, within three years of operation the College Department was named as one of the Top Three Performing Schools in the Caraga for the Kabalikat Award 2002 of TESDA. Additional courses were opened like 2-Year Computer-Based Accounting Technology, 2 Year Tourism Technology and 2 Year Computer-Technician. Speech subject was introduced in all departments complete with the state of the art speech facilities.

2003, the Accounting Department was established.

June 10, 2005, a four-storey concrete building was inaugurated. The Elementary Department was transferred from the Montinola Building to the main campus where the new building is situated. The new building housed the different offices, Preschool, High School, Mini Hotel, AVR and Faculty Rooms. Bachelor of Science in Computer Science was opened. Mini School bus was acquired.

2006, SMCC Angel Festival was introduced by Dr. Mausisa to the Michaelinian community.

2007, SMCC launches the SMCC Website

2008, College Department awarded by TESDA Region XIII as MODEL TVET Provider School in Agusan del Norte-Butuan City. The SMCC school logo was changed.

2009, Bureau of Immigration granted the school the accreditation permit to accept Foreign Students from Preschool to College. Commission on Higher Education granted the permit to operate Bachelor of Science in Hotel and Restaurant Management.

2010, Bachelor of Science in Information Technology and One Year Seafarer were opened.

2012, additional programs were opened the Bachelor of Science in Criminology, Bachelor of Science in Tourism Management, and the Housekeeping NCII. TESDA bundled programs were opened the Two year Hotel and Restaurant Technology with qualifications in Food and Beverage Services NC II and Housekeeping NCII, Two year Information Technology with qualifications in Computer Hardware Servicing NCII and Computer Programming NC IV and Two year Computer Electronics Technology with qualifications in Computer Hardware Servicing NC II and Consumer Electronics Servicing NC II.

2014, SMCC was granted by the Department of Labor and Employment (DOLE) the Certificate of Compliance on General Labor Standards, Occupational Safety and health Standards, and Child Labor-Free Establishment.

2015, Opening of additional TESDA Programs, the One Year Ship's Catering Services NC I (formerly Seafarer) and Visual Graphics NC III.

Permit to operate Senior High School was granted by the Department of Education offering Grades 11 and 12.

SMCC Higher Education Research Journal Book 1 was published and granted with ISBN and ISSN.

Miss Icee Galinato, Fourth (4th) placer in the Licensure Examination for Teachers Elementary Level September 2015 Board Examination.

2016, Opening of additional departments, the Learning Resource Department and Research and Publication Department. The Learning Resource Department includes the library, IM Center, and E-Library.

Construction of the 4-Storey SMCC Annex Building at the former Elementary Department Area.

2017, Opening of the SMCC DXSM FM. The only FM Station of the Diocese of Butuan.

2018, Opening of Bachelor of Physical Education, Bachelor of Technical-Vocational Teacher Education, Bachelor of Library and Information Science, Bachelor of Public Administration, Bachelor of Science in Entrepreneurship.

SMCC was certified with ISO 9001:2015. The first school in the Diocese of Butuan with ISO certification and the first school in the Caraga Region to be ISO certified 9001:2015 version.

Accepted as member of the Philippine Society for Quality.

Granted with the International Accreditation by the Asia Pacific for Events Managements of the United Kingdom last October 12, 2018. The first school in the Caraga Region and Northern Mindanao to be accredited.

Over-all Champion of the Kumbira Festival 2018, Mindanao-Wide HRM Competition at Cagayan de Oro City.

Awarded as Most Outstanding Technical Vocational Institution of TESDA Butuan City and Agusan del Norte for 2018.

Awarded as one of the Top Ten Finance Students of the Philippines for 2018.

Awarded as Outstanding Students of the Caraga Region for 2018.

At present, SMCC is getting Bigger, Better, Stronger, and Holier.