Background: Peru has increased substantially its domestic public expenditure in maternal and child health. Peruvian departments are heterogeneous in contextual and geographic factors, underlining the importance of disaggregated expenditure analysis up to the district level. We aimed to assess possible district level factors influencing public expenditure on reproductive, maternal, neonatal and child health (RMNCH) in Peru. Methods: We performed an ecological study in 24 departments, with specific RMNCH expenditure indicators as outcomes, and covariates of different hierarchical dimensions as predictors. To account for the influence of variables included in the different dimensions over time and across departments, we chose a stepwise multilevel mixed-effects regression model, with department-year as the unit of analysis. Results: Public expenditure increased in all departments, particularly for maternal-neonatal and child health activities, with a different pace across departments. The multilevel analysis did not reveal consistently influential factors, except for previous year expenditure on reproductive and maternal-neonatal health. Our findings may be explained by a combination of inertial expenditure, a results-based budgeting approach to increase expenditure efficiency and effectiveness, and by a mixed-effects decentralization process. Sample size, interactions and collinearity cannot be ruled out completely. Conclusions: Public district-level RMNCH expenditure has increased remarkably in Peru. Evidence on underlying factors influencing such trends warrants further research, most likely through a combination of quantitative and qualitative approaches.