In the spring 1998, the Shura Council (Board of Trustees) of the Islamic Center of Central Missouri surveyed the Muslim community in the city of Columbia soliciting its opinion on several projects to be undertaken - prioritization based on need and importance to the community. One of these projects was the establishment of a full-time Islamic School. The results of the survey listed establishment of an Islamic School as the first priority for the community. Accordingly, a decision was made in May 1998 to open a full-time Islamic School beginning fall 1998. A principal was hired to initiate the implementation of this decision.

Early summer of 1998, a three-member committee (including the Principal) was formed to work on facility, curriculum, textbooks, teacher recruitment, compilation of School handbook, and enrollment of students.
The School opened its doors in fall 1998 at 408 Locust Street with four grades: preschool, kindergarten, first and second grades. A multi-grade level teaching system was implemented for twenty-four students enrolled in the first year. These students were accommodated in two classes: ten students in preschool; and fourteen students in kindergarten, first and second altogether. Two Muslim certified teachers were hired for each class. The School was named “Islamic School of Columbia-Missouri”.

Every passing school year, thereafter, one grade was added until fifth grade. The School Education Board at the time decided not to go beyond fifth grade until better facilities were available and more qualified teachers hired.
The Islamic School of Columbia-Missouri has operated under the auspices of the Islamic Center of Central Missouri until December 2005. On January 10, 2006, the School was incorporated with the state of Missouri as an independent non-profit entity and has been operating as such since.

In June 2008, the Islamic School of Columbia-Missouri successfully completed an evaluation of its educational program, developed a plan for future educational improvements, and met all the current educational standards held by the Missouri Nonpublic School Accrediting Association (MNSAA), an affiliate of the National Federation of Nonpublic School State Accrediting Associations and recognized by the United States Office of Education and Council for the Advancement and Support of Education (CASE).