Greater school absenteeism is associated with numerous negative educational outcomes. We used a retrospective cohort design with linked administrative data on 296,422 children to examine the relationship between school absenteeism and child protection system (CPS) involvement. Children with substantiated maltreatment had 4.1 times more unexplained and problem absences than children with no CPS involvement. In multivariate analyses, children with substantiated maltreatment had significantly greater “chronic” truancy (OR = 3.41) and less “acceptable” levels of absences (OR = 0.74) compared to children with no CPS involvement. Greater absenteeism was seen for children with substantiated neglect and who had their first CPS notification earlier in life. Being in out-of-home care for 3+ years was a protective factor for children who had a CPS notification before age 5. Additional adversities had a strong additive effect with CPS involvement on absenteeism and chronic truancy. This study demonstrates the potential scope for reducing problem absenteeism and helps inform the public debate regarding how the type and timing of CPS involvement might ameliorate or exacerbate harm for children.