The role of peer relationships in a student's study wellbeing has been emphasised in research. However, the development of functional relationships with peers in educational settings cannot be taken for granted. In this study, we aimed to understand the variations in upper secondary school students' experiences of peer relationships in terms of sense of relatedness, cognitive and affective empathy skills and peer support for studying, and whether variation in these regards are related to study wellbeing. Two hundred and eighty Finnish upper secondary education students participated in the study. The data were analysed using latent profile analysis (LPA). Three distinct peer relationship profiles were detected among the students. Most of the students belonged to the functional peer relationship profile, while a minority belonged to either isolated or emotionally unrelated profiles. The students in the latter two profiles had a higher risk of experiencing challenges in study wellbeing in terms of reduced levels of study engagement and higher levels of study burnout symptoms. The findings imply that students in upper secondary education might need different kinds of support in building functional peer relationships. For example, some of them might benefit from learning empathy skills, while others might need support to meet their need for a sense of relatedness among peers.