In this longitudinal study, we examined the trajectories of sport and school burnout symptoms (exhaustion, cynicism, inadequacy) during the transition to lower secondary sport school among Norwegian student-athletes aged 13–14 years (n = 265; 58,5% males, 41,5% females). We also investigated how student-athletes’ gender and individual success expectations, and their parents’ reported levels of affection and success expectations, were associated with different burnout trajectories. Student-athletes completed associated questionnaires at the beginning and end of the first school year, while parents completed questionnaires at the end of the school year. Linear mixed models showed that sport and school burnout symptoms increased over the school year. Females reported higher baseline levels of sport burnout, and males lower baseline levels of school burnout. Low individual success expectations were associated with higher baseline levels of sport and school burnout, and increase in school burnout symptoms over time. High parental success expectations were associated with lower baseline levels of school-related exhaustion. Sport inadequacy increased for student-athletes whose parents reported either affection levels and success expectations that were either both high or both low. The results suggest that it is important that sport schools take the dual pressure student-athletes may experience into consideration, and provide them with adequate support during the transition to lower secondary education. In addition, interventions aimed at increasing parental knowledge of beneficial and harmful ways of involvement in student-athletes’ lives are needed to facilitate student-athlete wellbeing.