This study uses five waves of the Indonesian Demographic Health Surveys to analyse decentralisation and geographical inequality in health services delivery. Accounting for unobserved community-level heterogeneity with random effects and correlated random effects models, we link facility-based birth delivery to the period of decentralisation and Indonesia's major island groups using a pooled sample of 71,815 children. We also generate direct estimates of neonatal mortality from 1990 to 2007. The results show that the implementation of decentralisation has accorded with a marked expansion in both health service and outcome inequalities in Indonesia, at least with respect to neonates. Systemic funding failures for health and decision-space issues resulting from decentralisation are likely to have greater impact in disadvantaged regions where local capacity is weakest. The need to address these fundamental issues to reduce inequalities and improve general health outcomes appears supportable.