Objectives To assess the trends concerning utilisation of maternal and child health (MCH) services before, during and after the Ebola outbreak, quantifying the contribution of a reorganised referral system (RS). Design A prospective observational study of MCH services. Setting Pujehun district in Sierra Leone, 77 community health facilities and 1 hospital from 2012 to 2017. Main outcome measures MCH utililization was evaluated by assessing: (1) institutional deliveries, Cesarean-sections, paediatric and maternity admissions and deaths, and major direct obstetric complications (MDOCs), at hospital level; (2) antenatal care (ANC) 1 and 4, institutional delivery and family planning, at community level. Contribution of a strengthened RS was also measured. Results At hospital level, there is a significant difference between trends Ebola versus pre-Ebola for maternal admissions (7, 95% CI 4 to 11, p<0.001), MDOCs (4, 95% CI 1 to 7, p=0.006) and institutional deliveries (4, 95% CI 2 to 6, p=0.001). There is also a negative trend in the transition from Ebola to post-Ebola for maternal admissions (-7, 95% CI-10 to-4, p<0.001), MDOCs (-4, 95% CI-7 to-1, p=0.009) and institutional deliveries (-3, 95% CI-5 to-1, p=0.001). The differences between trends pre-Ebola versus post-Ebola are only significant for paediatric admissions (3, 95% CI 0 to 5, p=0.035). At community level, the difference between trends Ebola versus pre-Ebola and Ebola versus post-Ebola are not significant for any indicators. The differences between trends pre-Ebola versus post-Ebola show a negative difference for institutional deliveries (-7, 95% CI-10 to-4, p<0.001), ANC 1 (-6, 95% CI-10 to-3, p<0.001), ANC 4 (-8, 95% CI-11 to-5, p<0.001) and family planning (-85, 95% CI-119 to-51, p<0.001). Conclusions A stronger health system compared with other districts in Sierra Leone and a strengthened RS enabled health facilities in Pujehun to maintain service provision and uptake during and after the Ebola epidemic.