Objective: Although welfare in childhood and adolescence is of great public concern, individual or other resources have not been extensively studied in relation to wellbeing in schools. In this longitudinal study, factors that may promote girls’ or boys’ school wellbeing as well as factors that may have an adverse effect were assessed.

Methods: Altogether, 149 boys and 119 girls in public primary and secondary schools completed questionnaires twice, two years apart (T1 and T2). The impact of potentially promoting and potentially adverse factors at T1 were investigated in relation to school wellbeing at T2 using logistic regression.

Results: No gender differences were revealed in self-rated school wellbeing whereas factors associated with school wellbeing showed substantial gender differences. Boys who experienced necessary academic help from teachers were 2–3 times more likely to report good school wellbeing compared to other boys. For girls, perceived loneliness at school demonstrated a strong and negative association with school wellbeing both in crude and multivariable analyses.

Conclusions: There may be gender differences in predictors of students’ school wellbeing that health-promoting strategies need to take into account. Academic support from teachers, an example of resources in close surroundings, appears to be of great importance for boys. Among girls, perceived loneliness may indicate reduced school wellbeing. Later research must aim at identifying resources that prevent loneliness in school or ease the burdens of lonely students.