Although there is a wealth of research addressing the association between mental health and school absenteeism, there are calls for a better understanding of how mental health difficulties might predict SAPs (Egger et al., 2003; Finning et al., 2022; Ingul et al., 2019; Wood et al., 2012). The aim of this paper was to create a more nuanced understanding of SAPs by exploring how different constellations of mental health difficulties might be predictive of absenteeism in 9-year-olds. Using a sample of Irish 9-year-olds (N = 8570) from the Growing Up In Ireland Study (GUI’98), the research used latent class analysis (LCA) to identify combinations of mental health symptoms. Twenty items from the Strengths and Difficulty Questionnaire (SDQ) were used to measure a range of emotional and behavioural difficulties. The analysis yielded four mental health classes—High Risk of Emotional and Behavioural Difficulties (EBD), High Risk of Emotional Difficulties (ED), High Risk of Behavioural Difficulties (BD) and Low Risk of Emotional and Behavioural Difficulties (EBD). The study assessed whether rates of student absenteeism varied across different classes of mental health as identified through LCA and explored risk factors associated with different classes. Children in the high-risk mental health symptomology groups had significantly higher odds of absenteeism compared to the low-risk class and significantly greater odds of experiencing multiple family, school and demographic risk factors. The distinct profiles of mental health symptoms observed within the classes and their patterns of associations with risk factors and days absent indicated classes were theoretically distinct. The results illustrate the importance of recognising the relationship between mental health and school absenteeism in primary school children when developing early intervention strategies for SAPs. As one of the few studies to focus on 9-year-olds, the current study contributes to current knowledge on the complexities of emerging SAPs in primary school children.