This paper explores the social and emotional wellbeing and mental health complexities for Western Australian adolescents when they transition to a secondary boarding school. It presents data taken from a larger longitudinal quantitative study (3,462 students from 21 Catholic secondary schools) which included 76 male and 74 female boarding students while they were in Grades 7 and 8. This study used Chi-squared analyses to determine differences between boarders’ and non-boarders’ transition experiences, and separate multilevel regression models to determine whether boarder status was a predictor of social and emotional wellbeing and mental health following their transition to a secondary boarding school. Prior to attending a secondary school no difference existed between boarders and non-boarders with regards to social and emotional wellbeing and mental health. However, post-transition boarding students reported experiencing a significantly higher incidence rate of emotional difficulties and greater levels of depression, anxiety and stress than non-boarders. Significantly, it was found that emotional and mental health factors (e.g., anxiety, depression, emotional difficulties and stress) rather than the social factors (e.g., sense of connection with peers and school), mediated boarding students overall sense of wellbeing while they schooled away from home.