Burkina Faso has implemented a nationwide free healthcare policy (gratuité) for pregnant and lactating women and children under 5 years since April 2016. Studies have shown that free healthcare policies can increase healthcare service use. However, the emerging coronavirus disease 2019 pandemic, escalating insecurity and the political situation in recent years might have affected the implementation of such policies. No studies have looked at whether the gratuité maintained high service use under such changing circumstances. Our study aimed to assess the effects of gratuité on the utilization of facility-based delivery and curative care of children under 5 years in light of this changing context. We employed a controlled interrupted time series analysis using data from the Health Management Information System and annual statistical reports of 2560 primary health facilities from January 2013 to December 2021. We focused on facility-based deliveries and curative care for children under 5 years, with antenatal care and curative care for children over 5 years as non-equivalent controls. We employed segmented regression with the generalized least square model, accounting for autocorrelation and monthly seasonality. The monthly utilization rate among children under 5 years compared to those above 5 years (controls) immediately increased by 111.19 visits per 1000 children (95% CI: 91.12, 131.26) due to the gratuité. This immediate effect declined afterwards with a monthly change of 0.93 per 1000 children (95% CI: -1.57, -0.29). We found no significant effects, both immediate and long-term, on the use of maternal care services attributable to the gratuité. Our findings suggest that free healthcare policies can be instrumental in improving healthcare, yet more comprehensive strategies are needed to maintain healthcare utilization. Our findings reflect the overall situation in the country, while localized research is needed to understand the effect of insecurity and the pandemic at the local level and the effects of gratuité across geographies and socioeconomic statuses.