Introduction: Education provides a key pathway to economic opportunities, health, and well-being. Yet, limited or no locally available secondary schooling in remote Queensland Aboriginal and Torres Strait Islander communities requires more than 500 Indigenous students to transition to boarding schools. We report baseline quantitative data from the pilot phase (2016) of a 5-year study to explore a multicomponent mentoring approach to increase resilience and well-being for these students. Materials and methods: An interrupted time series design is being applied to evaluate levels of change in Indigenous students’ resilience and well-being. Surveys were collaboratively developed, with questions adapted from the Child and Youth Resilience Measure (CYRM-28), Kessler Psychological Distress Scale (K5), and questions which identified upstream risk factors for self-harm. They were completed by 94 students from five randomly selected schools (2 primary and 3 secondary) and one remote community. Results: Pre-transition, most primary school students reported high levels of resilience, but only a third reported moderate–high levels of psychological well-being. Secondary students attending a boarding school reported lower scores on resilience and psychosocial well-being measures. Students who transitioned back to community after being from boarding school reported a lower sense of connection to peers and family, and they reported even lower resilience and psychosocial well-being scores. Learning outcomes: Students have many strengths and can be adaptable, but their levels of resilience and psychosocial well-being are affected by the schooling transitions they are required to navigate. The findings are informing the development of intervention strategies to enhance student resilience and well-being.