Class teachers have a meaningful role in the life of primary school students as they are responsible for the majority of their students' instruction. Previous research has shown that teachers who make efforts to learn and develop in their work also promote their students' learning and well-being. This learning orientation is referred to in this study as teachers' professional agency. The well-being of students has been shown to be challenged in many ways already in primary school. However, we need more research on how primary school students experience well-being in classrooms in relation to their studies and whether their class teacher's professional agency relates to their well-being. We examined students' study well-being from two perspectives: study engagement and study burnout. Multilevel structural equation modelling was applied in the analysis to explore perceived study well-being in the classroom (student and class level) and its relation to class teachers' sense of professional agency. The results indicate that a high level of study burnout at the class level decreases students' study well-being over time and also challenges class teachers' sense of professional agency.