objective To assess the effect of a free healthcare policy for children under five years old implemented in Burkina Faso since April 2016, on the use of health care of non-malarial febrile illnesses (NMFI). methods To assess the immediate and long-term effect of the free healthcare policy in place, we conducted an interrupted time series analysis of routinely collected data on febrile illnesses from three urban primary health centres of Ouagadougou between 1 January 2015 and 31 December 2016. results Of the 39 046 febrile cases reported in the study period, 17 017 NMFI were included in the study. Compared to the period before the intervention, we observed an immediate, nonstatistically significant increase of 7% in the number of NMFI (IRR = 1.07; 95% CI = 0.75, 1.51). Compared to the trend that would have been expected in absence of the intervention, the results showed a small but sustained increase of 6% in the trend of monthly number of NMFI during the intervention period (IRR = 1.06; 95%CI = 1.01, 1.12). conclusion Our study highlighted an increase in the uptake of healthcare services, specifically for NMFI by children under five years of age, after the implementation of a free care policy. This analysis contributes to informing decision makers on the need to strengthen the capacities of healthcare centres and to anticipate the challenges of the sustainability of this policy. keywords non-malarial febrile illness, interrupted time series, long-term effect, free health care, Burkina Faso Sustainable Development Goals (SDGs): SDG 3 (good health and well-being), SDG 17 (partnerships for the goals)