We report a rare case of congenital lateral fistula of the upper lip associated with choanal atresia and nasal deformation. The characteristic clinical features of this case were a fistula located on the philtrum ridge at the columella base, associated with nasal deformation and choanal atresia. At 2 months of age, fistulectomy was performed with rhino-cheiloplasty under general anesthesia. Histological examination revealed that the resected fistula was lined by stratified squamous epithelium with sebaceous glands, which were not observed in deep sections of the fistula, and hair follicles.