Background In most African countries, indigents treated at public health centres are supposed to be exempted from user fees. In Africa, most of the available knowledge has to do with targeting processes in rural areas, and little is known about how to select the worst-off in an urban area. In rural communities of Burkina Faso, trials of participatory community-based selection of indigents have been effective. However, the process for selecting indigents in urban areas is not yet clear. Methods This study evaluates a community-funded participatory indigent selection process in both a formal (loti) and an informal (non-loti) neighbourhood in the urban setting of Burkina Faso's capital. This was an exploratory study to evaluate the processes and effectiveness of participatory targeting. We conducted individual interviews (n = 26) and analyzed secondary qualitative data (eight focus groups, 16 individual interviews). We also used the results of a socioeconomic survey (carried out by the Ouaga HDSS in 2011) of all the households established in the areas, including those of selected indigents. Results The coverage of indigent targeting was very low: 0.33% (loti) and 0.22% (non loti). In the non loti neighbourhood, the level of poverty among people selected was higher than the mean level of the poor who were not selected. Some indigents selected in the loti neighbourhood were not among the worst-off. The process was difficult to organize in the loti neighbourhood; people knew each other less well and were not very available, and there were cases of collusion. The process worked well in the non loti neighbourhood. Conclusions This intervention research provides new evidence about the feasibility of a community-based selection process in an urban setting in Africa by comparing two different urban settings. The participatory community-based selection process appeared to be suitable for the non loti neighbourhood, but other targeting strategies need to be found for loti areas. Specific budgets need to be allocated to increase the coverage of indigent targeting.