Mandaue Christian School Inc. was started in 1984 as a church-owned school of Mandaue City Baptist Church Inc. (MCBC). MCSI's first teacher was Ms. Evelyn Gillang (now Mrs. Evelyn Dayon), and she taught a class of only 18 pre-school children steadily increased each year. In 1995, there were considered the largest pre-school in Cebu in terms of population.

MCS was registered at the Securities at the Securities and Exchange Commission (SEC) on November 15, 1989. A permit to operate was granted by the Department of Education, Culture and Sports (DECS) in June 1985.

Although MCS only had four big classrooms and two play areas, it held 14 classes per day, with three sets of children using one room daily. 

MCSI became a member of the Association of Christian Schools International (ACSI) in 1991.

In 1995, Grades 1-4 were accomodated in MCBC's new two-storey church-school building. The MCS population skyrocketed from 375 to 670 learners for school year 1996-1997.

In May 31, 2001, the pre-elementary and elementary department were givengovernment recognition by tge Department of Education.

The high school department was established in 2005 with 67 students for 1st and 2nd year levels only. Government recognition was granted by the Department of Education to the high school department in May 2007.

MCSI was accepted as a member by the Association of Christian Schools, Colleges and Universities (AASCU) in 2010 and accredited by Fund Assistance to private Education (FAPE) in 2011.