School absenteeism among children and adolescents has been associated with a myriad of adverse outcomes. Despite a substantial amount of research on school attendance, our understanding of absenteeism in elementary-aged children with mental health difficulties is limited. The current study used a mixed-method sequential explanatory design to gain a better understanding of the links between children’s mental health symptoms, age, gender and school absenteeism. The study included two phases: Phase I presented a quantitative investigation of the links between absenteeism and mental health symptoms in a large sample (N = 750) of primarily White (74%) clinic-referred children aged 5–12 years. Phase II used a participant selection model and chart review design to garner a deeper understanding of how school absenteeism presents in children with mental health problems in the elementary years. Results suggested that internalizing symptoms were significantly related to school attendance problems, and this association worsens as children age and as internalizing symptoms increase in severity. Externalizing symptoms were associated with absenteeism as well, but these findings showed that school attendance problems were worse for younger children with low to moderate levels of externalizing symptoms. The qualitative chart review illustrates the complex interplay of school absenteeism and child mental health, particularly for children experiencing co-occurring internalizing and externalizing problems. Children often struggled academically and socially, with some exhibiting increasing levels of school refusal and truancy and others displaying aggressive behaviors resulting in suspensions. Future studies that examine additional contextual factors, such as school and family variables, with longitudinal cross-lagged models and diverse families are needed to develop a comprehensive understanding of causal associations and their impact on children’s school attendance across children’s development.