Overweight and obesity in childhood has reached epidemic levels, and their roles in physical and psychological health are now recognized. Recently, researchers have focused on the impact of these weight problems in health-related quality of life (HRQoL) domains, which are less investigated in children. This exploratory study examined the differences in HRQoL domains between a clinical group who were overweight/obesity treatment-seeking (n = 58) and a normal-weight group (n = 44) in a sample of 102 children, with a specific focus on school functioning and well-being. The second aim explored the link between our findings and other HRQoL dimensions. After controlling for sex and age, a multivariate analysis of variance showed lower levels in school functioning and well-being dimensions between overweight/obesity than normal-weight (F = 4.72; p < 0.05). Correlation analyses highlighted positive links between lower school functioning and well-being and lower levels of self-esteem (r = 0.308; p < 0.01) and social domains in terms of friendships (r = 0.522 ; p < 0.001) and family relationships (r = 0.561; p < 0.001) in children who were with overweight and obesity. This study discusses the implications of these findings in educational research and practices.