Background: This study aimed to explore the prevalence of chronic specific-site and multisite pain in adolescents and to investigate how it can possibly be determined by school-related factors. Methods: A population-based cross-sectional study was conducted in 2014 in Lithuania as a Health Behavior in School-Aged Children (HBSC) survey. The sample consisted of 5730 school children, aged 11, 13, and 15 years. The analyzed data focused on the school-related context (relations with family, peers, and teachers; school demand, satisfaction, and bullying) of adolescents and subjective health complaints. The relationships between social support and health complaint variables were estimated using multivariate analyses. Results: The most common subjective health complaint among respondents was a headache. Backache, headache, and stomachache were more common among girls than boys. All somatic complaints were expressed more in younger ages. Multisite complaints were more common among girls and were associated with age—older ones reported more complaints. School-related bullying, school demand, satisfaction, and social support were the most relevant and independent factors for multisite somatic complaints among adolescents.