In 1942, Hillcrest School was founded to provide a Christian education for missionary children by the Church of the Brethren Mission. Anticipation was keen. Clarence and Lucile Heckman had been remodeling and getting ready the storeroom and house on the CBM compound for this hoped for day of July 22, 1942. The teacher, Mary Dadison, welcomed 12 pupils to begin Hillcrest School, a new venture of the Church of the Brethren Mission. The school room, which also served as a house, had few pupils, with only two who were missionary children of CBM. Miss Dadison, both a nurse and teacher, had left the Garkida hospital to be the first teacher of the school.

There was a school room, a teacher, pupils, foster parents, food and even a bed, but no text books. The order had been placed early, but the books were lost at sea because of the war. A second order was placed. When it didn't arrive, a tracer brought a report: ship sunk. Then in May 1943, 80 different packages arrived. School was dismissed and all the children went with the staff to the post office to bring the first text books to Hillcrest. Books had never been more welcomed by either pupils or teachers.

In 1946, the school moved to the current location. In 1952 the enrollment was above 70. A special recognition service was held at St. Piran's church and 8th grade certificates were presented there to the 6 graduates

From the beginning, Hillcrest accepted pupils without regard to race or color. On March 29, 1947, "The Nigerian Daily Times", Lagos, carried an article "No Color Bar in Brethren Mission School." Other missions quickly developed an interest in Hillcrest. So, in 1955 the Sudan United Mission, Assemblies of God Mission and the United Missionary Society joined CBM's efforts. These original four grew to include the Missouri Synod Lutheran Mission (1963), the American Lutheran Mission (1964), the Nigerian Baptist Mission (1967), Mambilla Baptist Mission (1967), Sudan Interior Mission (1968), the Great Commission Movement (1982), and later both the United Methodist and the Wycliffe Bible Translators.

By November 1955 all arrangements for capital contributions and organization had been worked out and the first meeting of the Board of Governors of Hillcrest School was held. A constitution had been written, home boards had been contacted over and over and when the Board met for the first meeting there were present people from the 4 cooperating branches of S.U.M., Assemblies of God, U.M.S. and C.B.M. The cooperating mission shared in providing teachers and funds for capital improvements.

Hillcrest began as an elementary school, and high school classes were taken by correspondence until 1964. 1965 saw the first high school graduating class made up of eight students.

Hillcrest has continued to expand by adding classes, varsity sports and a variety of extracurricular activities. Student body populations have included students from many corners of the world, sometimes with as many as 34 different nations being represented on the campus at one time.