English
The English department teaches college-preparatory courses in Composition and Literature. All freshmen and sophomores at Johnson College Prep take a double English course load, with 9th graders taking Composition I and Multicultural Literature and 10th graders taking Composition II and World Literature. As the school grows, juniors will take English III with a focus on United States Literature, and seniors will take English IV or Advanced Placement English Literature and Composition.
 
Math
The Mathematics department currently includes a college-preparatory course structure that also includes double math courses for all freshmen and sophomores.  9th graders take Algebra I and Math Concepts, and 10th graders take Algebra II and Geometry. As the school grows, juniors will take Pre-Calculus and seniors will have the option of taking Calculus, a math elective, or Advanced Placement Calculus. 

Science
The Science Department is designed to provide each scholar with an outstanding foundation for college in the laboratory sciences. Freshmen scholars take Physics, sophomores take Chemistry, juniors take Biology, and seniors have a choice of a science elective or an Advanced Placement science course.  

Social Science
Scholars at Johnson College Prep prepare for the rigors of college with a strong foundation in the social sciences. Freshmen take Civics, sophomores take World History, juniors take United States History, and seniors take a social science elective or Advanced Placement World or US History.

Music
The music department offers scholars the opportunity to participate in an outstanding band program where all enrolled scholars learn the fundamentals of music theory and begin study of an instrument in their first year of the program. As they progress, scholars continue to practice in small group ensembles, sectionals, and large ensembles. Scholars perform several times a year for school events, family, and the public.

MCJROTC
Marine Corps Junior ROTC is an elective program where scholars learn strong work habits, self-discipline, physical fitness, and leadership skills. Scholars may participate in MCJROTC for up to four years, with each level of coursework increasing in depth of study and leadership opportunity.

Physical Education
Every scholar at Johnson College Prep College Prep participates in four years of physical education.  Scholars learn about health and exercise foundations that will lead to lifelong habits that promote wellness, healthy choices, and a commitment to strong physical fitness. 

Special Education
Johnson College Prep offers an outstanding support structure for all scholars with disabilities and learning differences. Core courses for scholars with disabilities are co-taught with a content teacher and licensed special educator in the same classroom, creating an inclusive setting for all scholars and allowing those with disabilities access to the same opportunities as their non-disabled peers.