Langerhans Cell Histiocytosis (LCH) is a rare proliferative disorder of the Langerhans cells, often affecting multiple organ systems and mimicking conditions like autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED). This case report details a 3-year-old male, who presented with submandibular swellings, nail abnormalities, seborrheic dermatitis and systemic involvement, initially diagnosed as APECED syndrome clinically. Fine-needle aspiration cytology (FNAC) and immunohistochemistry confirmed LCH. The patient was treated with vinblastine and prednisolone and showed marked improvement. This case emphasizes the importance of early, accurate diagnosis on FNAC to differentiate LCH from other mimicking conditions, enabling timely treatment and improved prognosis.