Background Becker’s nevus syndrome is a syndrome characterized by the presence of a Becker’s nevus with ipsilateral breast hypoplasia or hypoplastic defects of the muscle, skin, or skeleton. The nevus usually consists of a circumscribed, unilateral, irregularly shaped hyperpigmented macule, commonly occurring around the anterior upper trunk, with/without hypertrichosis and/or acneiform lesions. This rare syndrome has not been reported in our locality to the best of our knowledge. Case presentation We report the case of a 15-year-old Igbo female patient who presented to our pediatric endocrinology clinic, University of Nigeria Teaching Hospital, Enugu, with complaints of asymmetry of the breasts and hyperpigmented macules on the side. Based on her symptoms, diagnosis of Becker’s nevus syndrome was made. The diagnosis of Becker’s nevus syndrome is mostly clinical, based on the presence of a Becker’s nevus with ipsilateral breast hypoplasia or hypoplastic defects of the muscle, skin, or skeleton. In our patient, there was a Becker’s nevus with ipsilateral breast hypoplasia. This syndrome, belonging to the class of epidermal nevus syndromes, is very rare, and is usually benign. She was placed on spironolactone tablets 50 mg daily, which have been associated with an improvement in the size of the hypoplastic breast, and her fears were allayed. Conclusion This syndrome has not been reported in our locality to the best of our knowledge and, therefore, has a propensity for misdiagnosis by clinicians because of its rarity. We therefore report this to create awareness among clinicians regarding this condition that is associated with much psychosocial trauma among patients, and that can be easily managed with oral spironolactone.