All students in grades six through eight engage in a rigorous academic core program that utilizes a combination of Christian and secular textbooks to equip students for success in a college-preparatory high school program. Additionally, qualifying students may enroll in Honors courses which are designed to challenge the students academically by offering a quicker pace of instruction and more challenging extracurricular projects. All middle school students also participate in an activity rotation consisting of computer applications, library, Spanish, physical education, and fine arts instruction.

Every student in grades nine through twelve follows a college-preparatory academic track. Qualifying high school students may enter the Honors program, where the pace of instruction and the number of out-of-class projects are increased in all subject areas. Beginning in the tenth grade, students in the Honors program may also choose to enroll in Advanced Placement (AP) courses in various subject areas. A variety of additional elective courses are designed to meet the needs of a diverse student population. Both the regular and Honors academic tracks fulfill the requirements established by the Kentucky Department of Education for completion of the Pre-College Curriculum. Because Beth Haven Christian School is fully accredited through the Kentucky Department of Education, a diploma earned through BHCS is accepted by all colleges and universities nationwide. Additionally, qualifying BHCS high school students earn college scholarship funds through the Kentucky Educational Excellence Scholarship (KEES) program.