Self-harm and suicidal ideation in children and adolescents are common and are risk factors for completed suicide. Social exclusion, which can take many forms, increases the risk of self-harm and suicidal ideation. One important marker of social exclusion in young people is school absenteeism. Whether school absenteeism is associated with these adverse outcomes, and if so to what extent, remains unclear. To determine the association between school absenteeism and both self-harm (including completed suicide) and suicidal ideation in children and adolescents, we conducted a systematic review of observational studies. We conducted meta-analysis and report a narrative synthesis where this was not possible. Meta-analysis of cross-sectional studies showed that school absenteeism was associated with an increased risk of self-harm [pooled adjusted odds ratio (aOR) 1.37, 95% confidence interval 1.20–1.57, P = 0.01] and of suicidal ideation (pooled aOR 1.20, 95% CI 1.02–1.42, P = 0.03). A small number of studies showed that school absenteeism had a longitudinal association with both adverse outcomes. Heterogeneity in the exposure and outcome variables, study design and reporting was prominent and limited the extent to which it was appropriate to pool results. School absenteeism was associated with both self-harm and suicidal ideation in young people, but this evidence was derived from a small number of cross-sectional studies. Further research into the mechanisms of this association could help to inform self-harm and suicide prevention strategies at clinical, school and population levels.