The school follows Uganda’s national education structure, which is divided into two cycles: the Lower Secondary Education (Ordinary Level) and the Higher Secondary Education (Advanced Level). The Ordinary Level spans four years and leads to the Uganda Certificate of Education (UCE), where learners undertake a minimum of eight and a maximum of ten subjects. The Advanced Level, lasting two years, leads to the Uganda Advanced Certificate of Education (UACE) and allows learners to specialize in three principal subjects and two subsidiary subjects.
The school’s academic program is guided by key objectives of secondary education — instilling discipline, ethical and spiritual values, social responsibility, and self-reliance. Students are trained to develop scientific, technological, agricultural, and commercial skills essential for personal development and national growth. The curriculum also emphasizes problem-solving, critical thinking, leadership, and communication skills to prepare learners for higher education and future careers.

St. Charles Lwanga International Secondary School boasts modern and well-maintained facilities that support both academic and extracurricular excellence. The school features a reliable electricity supply with a standby generator, clean piped water, and over ten well-constructed buildings set on 10 acres of beautifully kept grounds. Learning resources include three fully equipped science laboratories, a new IT laboratory stocked with computers, and a well-resourced library. Other facilities include a spacious, fan-cooled main hall for assemblies and functions, sports fields for football, netball, and rugby, and clean, secure dormitories for both boys and girls. Additional amenities such as a well-stocked canteen, a sickbay with qualified staff, and a newly constructed kitchen ensure comfort, safety, and convenience for all students.