Purpose: Median cleft of upper lip is defined as any congenital vertical cleft through the midline of the upper lip. It is uncommon, its embryological pathogenesis remains unexplained to date. The authors hereby report a rare case of median cleft of the upper lip associated with enlarged frenulum and palatal mass. This case offers some understanding of the possible embryologic development of this anomaly. Methods: A 10-month-old boy born by normal vaginal delivery at full-term had a notch in the midline of the upper lip with widened philtrum along with enlarged median frenulum, alveolar cleft, and mass of the hard palate. We performed en bloc resection of the enlarged frenulum and palatal mass and cheiloplasty under general anesthesia. Results: Histological examination revealed that the frenulum and palatal mass was consisted of fibrous tissue with normal mucous membrane. The postoperative course was satisfactory. Conclusion: A rare case of median cleft of the upper lip with associated enlarged frenulum and palatal mass was presented with proper surgical management. The surgical technique includes marginal excision of the clefted epithelium and reconstruction of orbicularis oris muscle, in addition to en bloc resection of the palatal mass and frenulotomy.