Enabling children’s and youth’s well-being is widely valued by families and communities worldwide. However, there is no general agreement about the structure and measurement of well-being in schooling contexts, nor in particular for Indigenous students who comprise some of the most educationally disadvantaged populations in the world. We theorised a multidimensional student well-being model and the Multidimensional Student Well-being (MSW) instrument, grounded on recent research. We investigated its structure, measurement, and relation to correlates of well-being for a matched sample of 1,405 Australian students (Indigenous, N = 764; non-Indigenous, N = 641) at three time-points, 10–12 months apart. Analyses supported an a priori multidimensional model of 6 higher-order domains of well-being, represented by 15 first-order factors. This structure was invariant across Indigenous and non-Indigenous, male and female, and primary and secondary schooling levels. Correlates provided support for convergent and discriminant validity. There was a downward trend in well-being over time, which calls for attention to multidimensional domains of students’ well-being to promote healthy development throughout school life and beyond. The results support a multidimensional model of student well-being appropriate for primary and secondary schooling and both Indigenous and non-Indigenous students.