Congenital lip pits are characterized by sinuses or fistulas in the lips that can occur in isolation or as part of a genetic disorder. A 6-year-old girl with a right upper lip lesion present at birth presented with recurrent swelling and occasional erythema. Examination revealed a mildly swollen punctum at the right upper wet/dry vermillion with expressible serous drainage. There were no other phenotypic or cognitive concerns. The lesion was surgically excised using vertical wedge resection. The postoperative course showed well well-healed incision. The pathology report confirmed a lip pit. The family was referred to genetics for further evaluation. Van der Woude syndrome (VWS) is a genetic disorder associated with abnormal development of the paramedian lip. Most congenital lip pits are primarily found on the lower lips, with paramedian lip pits being the most common. Upper lateral lip pits with or without accompanying lip pits are considerably rarer. Though VWS is commonly associated with mutations in the interferon regulatory factor 6 or grainyhead-like protein 3 genes, ~25% of affected individuals lack an identified genetic etiology. A high index of suspicion for VWS is warranted if lip pits are present in the absence of other phenotypic abnormalities and should prompt genetic testing for interferon regulatory factor 6 and grainyhead-like protein 3 mutations. Multidisciplinary teams should consider patient self-esteem, quality of life, and potential family planning when deciding on surgical intervention for lip pits. Surgical management of pits should entail tissue-preserving techniques such as vertical wedge resection and inverted T-lip reduction to prevent whistle-lip deformity.