Mental health problems have increased among adolescents in Sweden and research suggests that contextual matters could be of importance over and beyond individual socio-demographic characteristics. One such social context is school, where both the student composition of the school and its support can influence student health. This study explored the distribution of psychosomatic health complaints (PHC) and perceived teacher support (PTS) as well as the association between PTS and PHC, across school segregated profiles. It also examined gender differences in these distributions and associations. The study design was cross-sectional, and data came from classroom-surveys within Stockholm municipality of ninth grade students in 2014 (n=4904). Linear regression analyse was applied. Results showed that average levels of PHC varied across school segregation profiles for girls, while PTS varied for both gender. PTS was negatively associated with PHC for all students, while the strength of association varied across school profiles to the benefit of students in the most privileged schools. Gender differences in these associations was also observed. Conclusions were that school context, based on the student composition of the school, and its provided support was linked to psychosomatic health complaints among students in Stockholm and that gender played a role in understanding pathways in these associations.