Almost half of patients have functional limitations after treatment of Buruli ulcer disease. Antibiotic treatment (along with surgery) was introduced in the National Program for Buruli ulcer in Benin in 2005. The aim of this study was to compare functional limitations in patients who were treated by antibiotics, surgery, or both, using a validated questionnaire. One hundred seventy-nine former patients in Lalo, Benin were retrieved and interviewed in their village. Hospital records were used to gather data about size of lesion at presentation and treatment provided. No significant differences in resulting functional limitations were found between the different treatments. Larger lesions (> 15 cm cross-sectional diameter) at presentation; lesions on a joint, muscular atrophy, and amputation were all associated with a higher risk for functional limitations. Advantages of antibiotic treatment may involve other domains, like costs of treatment or a change in help-seeking behavior.