Background: In 2016, a free healthcare policy (FHP) was implemented in Burkina Faso for children under the age of five. In our study, we aimed to determine the prevalence of careseeking for a fever in children under the age of five before and after the implementation of the FHP and to analyze the determinants of not seeking care under the FHP. Methods: The data of three nationally representative surveys were used to evaluate the trends of the prevalence of care-seeking. We performed a modified Poisson regression using a generalized estimating equation to determine the factors associated with not seeking care. Results: The prevalence for care seeking increased from 57.5% (95% CI, 54.2-60.8) in 2014 to 72.3% (95% CI, 68.1-76.2) in 2017. Children from the poor quintile were less likely to seek care when compared to children from the poorest quintile (prevalence ratio (PR) = 0.7 (95% CI, 0.5-0.9)). Caregivers who did not have messages regarding malaria in the past six months were more likely not to seek care (PR = 0.8 (95% CI, 0.7-0.9)). Caregivers of children aged 36-59 months were more likely not to seek care compared to those aged <12 months (PR = 1.6 (95% CI, 1.2-2.1)). Children from the Boucle du Mouhoun region (PR = 1.9 (95% CI, 1.2-3.2)) and the Centre-Est region (PR = 1.9 (95% CI, 1.2-3.0)) were more likely not to seek care compared to children from the Sud Ouest region. Conclusion: Our study showed an increase in the prevalence of care-seeking after the implementation of the FHP. Even if this is encouraging, these findings highlight the critical importance of non-financial barriers to care-seeking. Maintaining FHP and tackling the barriers should be considered by policy makers to increase care-seeking.