Setting: The Liberian counties of Bong, with performance-based financing (PBF) for all 36 public primary-care facilities, and Margibi, with no PBF for its 24 public primary-care facilities. Objective: To compare whether specific maternal and child health indicators changed in the two counties during the pre-Ebola (2013), Ebola (2014) and post-Ebola (2015) disease outbreak periods from July to September each year. Design: This was a cross-sectional study. Results: For pregnant women, the numbers of antenatal visits, intermittent preventive malaria treatments, human immunodeficiency virus (HIV) tests and facility-based births with skilled attendants all fell during the Ebola period, with decreases being significantly more marked in Margibi County. Apart from HIV testing, which remained low in both counties, these indicators increased in the post-Ebola period, with increases significantly more marked in Bong than in Margibi. The number of childhood immunisations decreased significantly in Bong in the Ebola period compared with the pre-Ebola period, but increased to above pre-Ebola levels in the post-Ebola period. There were markedly larger decreases in childhood immunisations in Margibi County during the Ebola period, which remained significantly lower in the post-Ebola period compared with Bong County. Conclusion: In a PBF-supported county, selected maternal and childhood health indicators showed less deterioration during Ebola and better recovery post-Ebola than in a non-PBF-supported county.