Fort Scott High School is an accredited secondary school for grades nine through twelve. Students are enrolled in eight academic classes plus a seminar time for additional teacher assistance as well as school clubs, activities and assemblies. Classes meet in a combination of block and traditional scheduling. A-day classes meet on Monday and Wednesday for 81 minutes each and B-classes meet on Tuesday and Thursday also for 81 minutes, with an additional 42 minutes each day for seminar. Fridays follow a C schedule with each class meeting for 44 minutes and no seminar.

Classes are offered in two curriculum tracks. The Kansas Regents Curriculum prepares students to enter universities in Kansas and beyond. The Tech Prep Curriculum is for students entering a community college or moving directly into the work force. A physical education program is offered and includes boys and girls fitness classes. Students are also offered opportunities in career pathways and building trades. Both special education and gifted education are provided at FSHS.

FSHS offers a wide array of electives and extra curricular activities. Electives include music, visual arts, automotive, foreign language, agriculture, drafting and construction as well as Advanced Placement classes. Activities include numerous clubs and sports, which can be seen by clicking on the link to the left.