After the 2022-2023 Sudan virus (SUDV) disease outbreak in Uganda, we studied SUDV persistence in nonhuman primates that had survived acute infection without therapeutic intervention. We identified SUDV persistence in the vitreous chamber and immediately adjacent tissue in the eyes as well as in the seminiferous tubules in the testes but not in common target organs typically infected during the acute phase of disease. Specifically, SUDV persists primarily in macrophages in the eyes and Sertoli cells in the testes. Ocular and testicular SUDV persistence in nonhuman primates is accompanied by tissue damage, including inflammatory cell invasion. Our study suggests that long-term follow-up efforts are needed to reduce possible recrudescent disease and reignition of outbreaks caused by virus persistence in human survivors of SUDV infection.