Post-pandemic school absence is an increasing concern for governments worldwide. Absence is associated with poor academic outcomes and long-term illness (physical and mental). Absenteeism increases the risk of financial difficulties in adulthood and involvement in the criminal justice system. We hypothesized that early childhood problems might be an antecedent of absenteeism. We tested this hypothesis by investigating the pre-pandemic association between school readiness and persistent absenteeism using a population-linked dataset. Analyses included 62,598 children aged 5–13 years from the Connected Bradford database (spanning academic years 2012/13 to 2019/20). Special educational needs status, English as an Additional Language status, socioeconomic status, sex and ethnicity were covariates significantly associated with persistent absenteeism. Children who were not ‘school ready’ had increased odds of being persistently absent later in their education journey after controlling for these covariates. School readiness was associated with even greater odds of being persistently absent over two or more years. These findings show (i) the seeds of absenteeism are sown early in childhood; (ii) absenteeism shows the hallmark of structural inequities; and (iii) the potential of ‘school readiness’ measures to identify children at risk of long-term disengagement from the education system.