An extremely rare patient of congenital midline sinus of the upper lip in a 2-year-old boy is presented. The sinus was located on the midline of the philtrum just below the base of the columella. Surgical removal of the sinus was performed via an extra- and inraoral approach. Histopathological examination of the resected sinus revealed it to be lined by keratinized stratified squamous epithelium with sebaceous glands and hair follicles. Three postulates can account for the formation of the congenital midline sinus of the upper lip: the fusion theory, the merging theory, and the invagination theory. However, the etiology of this rare abnormality remains obscure.