Hypogonadotropic hypogonadism is a condition resulting from dysfunction of the hypothalamic-pituitary-gonadal axis, leading to impaired production of sex hormones and disrupted development. In many cases, an accurate diagnosis is unobtainable. This report presents the case of a 17-year-old patient with an incidental diagnosis of delayed puberty who underwent a full diagnostic procedure, which did not reveal a clear cause of hypogonadism. Following treatment with gonadotropins, proper testosterone levels, full masculinisation, and psychical well-being were achieved. This case highlights that accurate examinations during standard paediatric visits are crucial for the diagnosis of delayed puberty and other development abnormalities. Diagnosing hypogonadotropic hypogonadism is challenging, and determining a definitive diagnosis is often difficult. Individualised treatment with gonadotropins or testosterone is necessary for achieving sexual development and proper social functioning.