IntroductionThe rising rate of incarceration in Australia, driven by high reoffending, is a major public health problem. Problematic drug use is associated with increasing rates of reoffending and return to custody of individuals. Throughcare provides support to individuals during imprisonment through to post-release, improving both the transition to community and health outcomes post-incarceration. The aim of this study is to evaluate the Connections Programme (CP) that utilises a throughcare approach for release planning of people in prison with a history of problematic drug use. The study protocol is described.Methods and analysisPopulation-based retrospective cohort study. The study will use record linkage of the Connections dataset with 10 other New South Wales (NSW) population datasets on offending, health service utilisation, opioid substitution therapy, pregnancy, birth and mortality. The study includes all patients who were eligible to participate in the CP between January 2008 and December 2015 stratified by patients who were offered CP and eligible patients who were not offered the programme (non-CP (NCP)). Propensity-score matching will be used to appropriately adjust for the observable differences between CP and NCP. The differences between two groups will be examined using appropriate univariate and multivariate analyses. A generalised estimating equation approach, which can deal with repeat outcomes for individuals will be used to examine recidivism, mortality and other health outcomes, including perinatal and infant outcomes. Survival analysis techniques will be used to examine the effect of the CP by sex and Indigenous status on the ‘time-to’ health-related outcomes after adjusting for potential confounders.Ethics and disseminationEthical approval was received from the NSW Population and Health Services Research Ethics Committee, the Justice Health and Forensic Mental Health Network Human Research Ethics Committee, the Aboriginal Health and Medical Research Council Ethics Committee, the Corrective Services NSW Ethics Committee and the University of Technology Sydney Human Research Ethics Committee.