Adolescent development involves a complex interplay between genetics, biology, and social and emotional relationships within multiple contexts of home, school and the broader community. The transition from primary to secondary school, coupled with the onset of puberty, can therefore be a difficult period for young people to negotiate at a critical period of their developmental pathway. Using a social ecological perspective, this article examines the impact of the transition experience on adolescent social and emotional health, both immediately following transition to secondary school and at the end of the first year in this new school environment. This 1-year prospective study involving 1,500 Australian Grade 8 secondary school students found that 31% of students in the sample experienced a "difficult" or "somewhat difficult" transition to their new school. This third of the student sample were consequently more likely to experience poorer social and emotional health, including higher levels of depression and anxiety at the end of their first year of secondary school, while controlling for these variables at the time of transition. A central message from this work exemplifies the urgent need for a longitudinal intervention trial to develop best practice guidelines for activities that help ameliorate the negative impact a change in education context can create for adolescents negotiating a rapid metamorphosis from childhood to adulthood.