Abstract Background Numerous studies have demonstrated a strong link between child maltreatment and subsequent youth offending, leading to calls for early intervention initiatives. However, there have been few whole-population studies into the dimensions of statutory child maltreatment responses that can inform these programs. The aim of this study was to investigate the sex-specific association between level and timing of child protection system (CPS) contact and youth offending. Methods This retrospective cohort study used linked individual-level records from multiple agencies, for 10,438Aboriginal children born in the Northern Territory between 1999 and 2006. The outcome measure was the first alleged offence. Key explanatory variables were level (no contact through to out-of-home care) and timing (0–4 years, 5–9 years, or both) of CPS contact. The Kaplan–Meier method was used to estimate cumulative incidence and a flexible parametric survival model to estimate hazard ratios (HR). Results Children with no record of CPS contact before age 10 had the lowest cumulative incidence of first alleged offence by age 18 (boys: 23.4% [95%CI:21.0–26.1]; girls: 6.6% [95%CI:5.3–8.2]) and those with a record of out-of-home care the highest CI (boys: 45.5% [95%CI:37.0–54.9]; girls: 18.6% [95%CI:13.0–26.2]). The association of CPS contact with the relative risk of a first alleged offence was greatest for children aged 10–13 years and decreased with age. Timing of CPS contact was also associated with increasing cumulative incidence. The relative risk for first alleged offence was generally higher for children with CPS contact, of any type, during both developmental phases including notifications during both phases (boys, HR at age 11: 8.9 [95%CI:4.2–17.2]; girls, HR at age 11: 13.7 [95%CI:3.8–48.9]) and substantiations during both phases (boys, HR at age 11: 17.0 [95%CI:9.6–30.0]; girls, HR at age 11: 54.1 [95%CI:18.1–162]). Conclusion The increased risk of offending associated with level and timing of early CPS contact highlights opportunities for a differentiated public health response to improve life trajectories for children and to reduce youth crime. Although children with unsubstantiated notifications of maltreatment do not meet the criteria for a statutory CPS response, the higher risk of offending among these children supports their inclusion in targeted preventive interventions.