Fifty years after the last report of Mycobacterium ulcerans infections (Buruli ulcer [BU]) in Kasongo Territory, Maniema Province, Democratic Republic of Congo (DRC), we conducted a small-scale cross-sectional survey to assess if this historical BU focus was still active and if so to explore the disease epidemiology. Seventy-five active and inactive BU cases were identified on clinical grounds of which two of 28 BU active cases were laboratory confirmed. We used a modified BU02 form to reconstruct the local disease dynamics and we believe that the horrific conflict in eastern DRC and exceptional flooding were the most likely causes of the re-emergence of the disease. There is a need in the DRC to decentralize and integrate surveillance and control activities at local level to increase the effectiveness of patient management.