Although the number of direct Ebola-related deaths from the 2013 to 2016 West African Ebola outbreak has been quantified, the number of indirect deaths, resulting from decreased utilization of routine health services, remains unknown. Such information is a key ingredient of health system resilience, essential for adequate allocation of resources to both ‘crisis response activities’ and ‘core functions’. Taking stock of indirect deaths may also help the concept of health system resilience achieve political traction over the traditional approach of disease-specific surveillance. This study responds to these imperatives by quantifying the extent of the drop in utilization of essential reproductive, maternal and neonatal health services in Sierra Leone during the Ebola outbreak by using interrupted time-series regression to analyse Health Management Information System (HMIS) data. Using the Lives Saved Tool, we then model the implication of this decrease in utilization in terms of excess maternal and neonatal deaths, as well as stillbirths. We find that antenatal care coverage suffered from the largest decrease in coverage as a result of the Ebola epidemic, with an estimated 22 percentage point (p.p.) decrease in population coverage compared with the most conservative counterfactual scenario. Use of family planning, facility delivery and post-natal care services also decreased but to a lesser extent (−6, −8 and −13 p.p. respectively). This decrease in utilization of life-saving health services translates to 3600 additional maternal, neonatal and stillbirth deaths in the year 2014-15 under the most conservative scenario. In other words, we estimate that the indirect mortality effects of a crisis in the context of a health system lacking resilience may be as important as the direct mortality effects of the crisis itself.