Performance-Based Financing (PBF) is a promising approach to improve health system performance in developing countries, but there are concerns that it may inadequately address inequalities in access to care. Incentives for reaching the poor may prove beneficial, but evidence remains limited. We evaluated a system of targeting the poorest of society (‘indigents’) in a PBF programme in Cameroon, examining (under)coverage, leakage and perceived positive and negative effects. We conducted a documentation review, 59 key informant interviews and 33 focus group discussions with community members (poor and vulnerable people—registered as indigents and those not registered as such). We found that community health workers were able to identify very poor and vulnerable people with a minimal chance of leakage to non-poor people. Nevertheless, the targeting system only reached a tiny proportion (≤1%) of the catchment population, and other poor and vulnerable people were missed. Low a priori set objectives and implementation problems—including a focus on easily identifiable groups (elderly, orphans), unclarity about pre-defined criteria, lack of transport for identification and insufficient motivation of community health workers—are likely to explain the low coverage. Registered indigents perceived improvements in access, quality and promptness of care, and improvements in economic status and less financial worries. However, lack of transport and insufficient knowledge about the targeting benefits, remained barriers for health care use. Negative effects of the system as experienced by indigents included negative reactions (e.g. jealousy) of community members. In conclusion, a system of targeting the poorest of society in PBF programmes may help reduce inequalities in health care use, but only when design and implementation problems leading to substantial under-coverage are addressed. Furthermore, remaining barriers to health care use (e.g. transport) and negative reactions of other community members towards indigents deserve attention.