Given the importance of schools as socializing institutions, a key dimension of children’s subjective well-being (SWB) is their perception of school-related aspects. This study complements previous literature on various determinants of children’s SWB by focusing on students with special educational needs (SEN). Due to academic challenges, stigmatization, and exclusion, they are at risk of experiencing reduced SWB. With the implementation of inclusive education around the globe, students with SEN are more frequently enrolled in regular schools, and a question arises regarding how students with SEN assess their school-related SWB in inclusive settings. Drawing on longitudinal data from the National Educational Panel Study in Germany (NEPS) we systematically investigate the effect of the SEN status on various facets of school-related SWB measured in Grade 4 of primary school. Applying a propensity score matching approach, we contrast children with SEN status to children without SEN status who are comparable in a rich set of observed confounding variables. We find that at the end of primary school, students with SEN report being less satisfied with life in general, being less satisfied with school and their friends than their comparable counterpart without SEN. Moreover, they experience more tiredness and feelings of loneliness, and show lower levels of learning enjoyment and task mastering. The potential mechanisms leading to lower school-related SWB are discussed.