In 1994, prevalence and incidence of epilepsy were high in the Itwara onchocerciasis focus (western Uganda), and cases of nodding and Nakalanga syndrome were documented. Onchocerciasis transmission was interrupted successfully in 2001. 17 years later, we re-investigated the epilepsy burden in this area. From Dec 11 to Dec 15, 2018, a door-to-door survey was done in the three villages (Kabende Centre, Masongora South, and Rwesenene) with the highest epilepsy rates in 1994 to identify people with suspected epilepsy. Epilepsy diagnoses were confirmed by an interview and physical examination by a study clinician. The prevalence and incidence of epilepsy were measured using methods consistent with those used in 1994. Results from 2018 were compared with those from 1994. The overall crude prevalence of epilepsy in the study villages decreased from 3·0% (35 of 1169) in 1994 to 1·2% (27 of 2325) in 2018 (p=0·0002), with a concomitant decrease in the proportion of people with epilepsy with unknown cause (p=0·037). Between 1994 and 2018, the overall incidence of epilepsy decreased from 418 cases per 100 000 person-years (95% CI 265–626) to 73 new cases per 100 000 person-years (32–114; p<0·0001); this reduction was more pronounced for cases having the first seizure between ages 3 years and 18 years (p<0·0001). No new case of nodding or Nakalanga syndromes had occurred since the interruption of onchocerciasis transmission. Our findings support the existence of a negative association between onchocerciasis elimination and epilepsy burden in previously hyperendemic areas. Therefore, onchocerciasis elimination efforts should be intensified in endemic regions with a high prevalence of epilepsy, which might reduce the burden of epilepsy. Flemish University Development Cooperation and the European Research Council.