Apart from the Academic departments, Nakeel Boys High School has other departments such as:
- Boarding Department – In charge of boarding aspects of the students, kitchen staff, dining, food preparation among others.
- Welfare Department – In charge of teachers’ welfare.
- Guidance and Counselling Department – Dealing with counselling of students and offering alternative correctional measures as opposed to punishment.
- Games Department – Consisting of the various games played in school, that is, football, handball, volleyball, badminton, lawn tennis, table tennis, basketball, swimming, athletics, field events among others.