Background <p>Becker nevus syndrome is a rare epidermal nevus syndrome defined by the co-occurrence of a Becker nevus with various cutaneous, muscular, and skeletal anomalies. </p> Case presentation <p>Here, we present a case of Becker Nevus Syndrome (BNS) with segmental alopecia areata and ipsilateral musculoskeletal anomalies. A four-year-old boy presented with a hyperpigmented patch on his left leg, present since birth, and a size discrepancy on the same leg, while areas of segmental alopecia areata were observed in the vertex, occipital, and retroauricular regions of the right half of his scalp. Clinical, radiological, and histopathological evaluations led to the diagnosis of Becker Nevus Syndrome with segmental alopecia areata and musculoskeletal anomalies.</p> Conclusion <p>Our case demonstrates the phenotypic heterogeneity of BNS, the possibility of early presentation, the absence of hypertrichosis, and the potential for unusual findings such as segmental alopecia areata. Therefore, in patients with suspected BNS, it is essential for the clinician to carefully evaluate the patient for possible associated systemic anomalies and to provide multidisciplinary referral.</p>