A 9-year-old girl with a medical history significant for ectrodactyly ectodermal dysplasia clefting (EEC) syndrome was referred for evaluation of congenital left-sided epiphora. The patient had undergone successful right external dacryocystorhinostomy at age 5 to treat congenital right-sided epiphora. On examination, several ocular anomalies were noted, including absence of the upper eyelid puncta, absence of the left inferior punctum, a left lacrimal fistula opening at the left caruncle, increased left tear lake, bilateral hypoplastic meibomian glands, mild conjunctival injection, and thin eyelid cilia and brow hair. Systemic findings included cleft lip and palate status-post repair, ectrodactyly of the hands and feet, adontia and microdontia, a pointed nose, and lightly pigmented, dry hair and skin. The patient underwent examination under anesthesia and left conjunctivodacryocystorhinostomy with insertion of a Jones tube with resolution of lacrimation postoperatively. To the authors’ knowledge, this is the second report detailing management of congenital lacrimal anomalies in EEC syndrome, and the first describing management of punctal atresia with conjunctivodacryocystorhinostomy and Jones tube placement.