Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is a congenital eyelid syndrome. Several associations, including the horizontal displacement of the puncta, canalicular stenosis, and ectropion have been so far described. Herein, we report a one-year-old boy presented to the Oculoplastic Clinic of Farabi Eye Hospital with complaint of watery discharge from both eyes since his birth. Based on the general appearance, the diagnosis of BPES was made. Mild tear regurgitation from the inferior punctum was noted. Detailed examination showed bilateral superior punctal agenesis with coloboma of both upper eyelids and lateral displacement of the inferior puncta. Multiple unsuccessful attempts of probing were suggestive of the presence of NLDO. The patient was managed by performing canaliculodacryocystorhinostomy. Osteotomy was performed to pass the canalicular and nasolacrimal obstruction followed by a successful canaliculoplasty. Finally, the lacrimal drainage system was intubated with a mono-Crawford from the inferior punctum into the nasal cavity. On the 1st-month follow-up visit, the complaint of watery discharge was resolved. This is an extremely rare report of nasolacrimal duct and sac anomaly in a patient with blepharophimosis. Thus, we recommend the evaluation of the nasolacrimal drainage system in these patients after the first month of birth.