Background Measuring progress towards financial risk protection for the poorest is essential within the framework of Universal Health Coverage. The study assessed the level of out-of-pocket expenditure and factors associated with excessive out-of-pocket expenditure among the ultra-poor who had been targeted and exempted within the context of the performance-based financing intervention in Burkina Faso. Ultra-poor were selected based on a community-based approach and provided with an exemption card allowing them to access healthcare services free of charge. Methods We performed a descriptive analysis of the level of out-of-pocket expenditure on formal healthcare services using data from a cross-sectional study conducted in Diebougou district. Multivariate logistic regression was performed to investigate the factors related to excessive out-of-pocket expenditure among the ultra-poor. The analysis was restricted to individuals who reported formal health service utilisation for an illness-episode within the last six months. Excessive spending was defined as having expenditure greater than or equal to two times the median out-of-pocket expenditure. Results Exemption card ownership was reported by 83.64% of the respondents. With an average of FCFA 23051.62 (USD 39.18), the ultra-poor had to supplement a significant amount of out-of-pocket expenditure to receive formal healthcare services at public health facilities which were supposed to be free. The probability of incurring excessive out-of-pocket expenditure was negatively associated with being female (beta = - 2.072, p = 0.00, ME = - 0.324; p = 0.000) and having an exemption card (beta = - 1.787, p = 0.025; ME = - 0.279, p = 0.014). Conclusions User fee exemptions are associated with reduced out-of-pocket expenditure for the ultra-poor. Our results demonstrate the importance of free care and better implementation of existing exemption policies. The ultra-poor's elevated risk due to multi-morbidities and severity of illness need to be considered when allocating resources to better address existing inequalities and improve financial risk protection.