Background: The purpose of the study was to describe the pattern of presentation of congenital ocular anomalies (COAs) among children seen at the, Department of Ophthalmology (Guinness Eye Centre), Lagos University Teaching Hospital, Lagos, Nigeria). Methods: A retrospective chart review of children below the age of 16 years who were diagnosed of any type of congenital ocular anomaly at the Pediatric Ophthalmology Clinic of Lagos University Teaching Hospital, Lagos, Nigeria between January 2012 and December 2018 was done. Information concerning the age at presentation, gender, affected eye(s), visual acuity, and type of congenital anomaly was retrieved from the case files. Results: Seven hundred and forty-five eyes of 470 patients with congenital anomalies which constituted 13.6% of all the new pediatric ophthalmic consultations were studied. Two hundred and seventy-five (58.5%) children had bilateral ocular involvement, while 262 (55.7%) presented within the first year of life. The median age was 0.92 years with an interquartile range of 2.67 years. There were 255 (54.5%) males, with a male-to-female ratio of 1.2:1. Congenital cataract was the most common congenital ocular anomaly documented in 224 (30.1%) eyes of 133 patients. This was followed by congenital squint (131 eyes, 17.6%), congenital glaucoma (91 eyes, 12.2%), and corneal opacity (52 eyes, 7.0%). Overall, cataract, squint, glaucoma, corneal opacity, nasolacrimal duct obstruction, and ptosis accounted for 79.0% of the COAs documented in this study. Conclusion: COAs accounted for 13.6% of pediatric ophthalmic consultations in this study. Congenital cataract, squint, glaucoma, corneal opacity, nasolacrimal duct obstruction, and ptosis were the most common COAs observed.