<p>As students progress through grades, school absences (SA) tend to rise, a trend observed alongside the growing importance of peer relations. While much research has examined SA, less is known how different reasons for SA and peer relations are related. This study focused on Grade 7 students (<i>N</i> = 838) and their experiences after the transition from primary to lower secondary school. The data were collected at two points during Grade 7, in the autumn (T1) and in the spring (T2). Ordinal logistic regression was used to model both a) the relationships among the three student-reported SA reasons (sickness, truancy and other reasons) and b) the links between these SA reasons and two different aspects of peer relationships (peer-rated peer preference and a self-reported closeness with best friends at school). The results showed that SA due to sickness, truancy and other reasons predicted each other in Grade 7. Moreover, a higher level of peer preference was related to lower SA due to sickness and truancy in the autumn of Grade 7, but higher SA due to other reasons in the spring of the same school year. A higher perceived closeness with best friends at school was related to lower truancy at both time points. This study highlights the importance of understanding the links between different reasons for SA and the protective effect of positive peer relations on SA due to sickness and truancy after the transition to lower secondary school.</p>