Langerhans cell histiocytosis (LCH) is a rare disease that occurs mainly in children. It has several forms of clinical presentation. Early diagnosis is important for better results. A 17-year-old male patient presented with right sharp shoulder pain for 2 months. Magnetic resonance image (MRI) of the shoulder showed an expansile osseous lesion in the anterosuperior spine of the right scapula with significant edema that causes compression of the subscapular neurovascular bundle. A CT scan and X-rays were also performed. Overall, all the images suggested a lesion compatible with chondroblastoma; however, the pathology images documented a Langerhans cell histiocytosis with a mutation in the V600E/E2/D in the 15 exon of the BRAF gene. LCH is a difficult diagnosis, especially in cases where clinical presentation is not the most common. This case is unique as the lesion developed not only in the scapula which has a 3% prevalence in LCH, but also had radiographic and MRI characteristics of a chondroblastoma more than the typical LCH lesion. Additionally, it was accompanied by a BRAF V600E mutation which is uncommon in LCHs bone cases.