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An increased prevalence of epilepsy has been reported in many onchocerciasis endemic areas. Between July 2014 and February 2016, house-to-house epilepsy prevalence surveys were carried out in the Bas-Uele, Tshopo and Ituri province of the Democratic Republic of the Congo, in areas with a high level of onchocerciasis endemicity. Of 12, 408 people examined in the different health areas 407 (3.3%) were found to have a history of epilepsy. A nested case control analysis demonstrated that before the appearance of epilepsy, compared to the same life period in controls, persons with epilepsy were around two times less likely to have taken Ivermectin than controls. Our data suggests that Ivermectin protects against epilepsy in an onchocerciasis endemic region. However, a prospective population based intervention study is needed to confirm this.