Headaches and neck pain are reported to be among the most prevalent musculoskeletal complaints in the general population. A significant body of research has reported a high prevalence of headaches and neck pain among adolescents. Sitting for lengthy periods in fixed postures such as at computer terminals may result in adolescent neck pain and headaches. The aim of this paper was to report the association between computer use (exposure) and headaches and neck pain (outcome) among adolescent school students in a developing country. A cross-sectional study was conducted and comprehensive description of the data collection instrument was used to collect the data from 1073 high-school students. Headaches were associated with high psychosocial scores and were more common among girls. We found a concerning association between neck pain and high hours of computing for school students, and have confirmed the need to educate new computer users (school students) about appropriate ergonomics and postural health.