IntroductionDespite renewed commitment to universal health coverage and health system strengthening (HSS) to improve access to primary care, there is insufficient evidence to guide their design and implementation. To address this, we conducted an impact evaluation of an ongoing HSS initiative in rural Madagascar, combining data from a longitudinal cohort and primary health centres.MethodsWe carried out a district representative household survey at the start of the HSS intervention in 2014 in over 1500 households in Ifanadiana district, and conducted follow-up surveys at 2 and 4 years. At each time point, we estimated maternal, newborn and child health coverage; economic and geographical inequalities in coverage; and child mortality rates; both in the HSS intervention and control catchments. We used logistic regression models to evaluate changes associated with exposure to the HSS intervention. We also estimated changes in health centre per capita utilisation during 2013 to 2018.ResultsChild mortality rates decreased faster in the HSS than in the control catchment. We observed significant improvements in care seeking for children under 5 years of age (OR 1.23; 95% CI 1.05 to 1.44) and individuals of all ages (OR 1.37, 95% CI 1.19 to 1.58), but no significant differences in maternal care coverage. Economic inequalities in most coverage indicators were reduced, while geographical inequalities worsened in nearly half of the indicators.ConclusionThe results demonstrate improvements in care seeking and economic inequalities linked to the early stages of a HSS intervention in rural Madagascar. Additional improvements in this context of persistent geographical inequalities will require a stronger focus on community health.