Colobomatous cyst of the eye (microphthalmos with cyst) is a congenital abnormality that consists of a small, malformed eye with a coloboma through which a cystic herniation of glial tissue protrudes into the orbit. The precise causes of a colobomatous cyst are not known and the anomaly is usually detected at birth affecting one or both orbits. We present a 2-year-old girl with right eye swelling since birth. The swelling had been gradually increasing in size with an associated loss of vision in the eye. Examination of the right eye showed an enlarged, well-defined, oval-shaped trans-illuminating cystic mass lesion protruding out of the right orbital cavity with skin covering. Magnetic resonance imaging revealed a well-defined oval-shaped cystic mass lesion that was hypointense on T1 weighted and hyperintense on T2-weighted image protruding out of the right orbital cavity. The ipsilateral globe was microphthalmic, and was displaced, and compressed posteriorly by the cystic mass lesion. The remaining orbital structures, including the optic nerve, were also compressed and difficult to visualize. Based on the clinical and radiological features, a diagnosis of orbital colobomatous cyst was established. She had enucleation with total lesion excision for treatment. This case is reported because of its rarity and associated developmental anomalies. Its management in the African setting is challenging, but feasible with early patient presentation and improved health facilities.