Objective: The objective of this study was to study the presentation of isolated hypogonadotropic hypogonadism (IHH) in the youngest reported case till date. Introduction: Isolated hypogonadotropic hypogonadism is a clinical syndrome associated with gonadal dysfunction and altered pituitary gonadotropin levels, while the other pituitary hormones remain within normal limits. No olfactory symptoms were present hence differentiating it from congenital hypogonadotropic hypogonadism (CHH). Case presentation: A 16-year-old girl presented with primary amenorrhea, delayed breast and pubic hair development, and low gonadotropins, but other anterior pituitary hormones were within normal limits. Imaging of the hypothalamic–pituitary region was normal. Hormonal therapy was started to induce secondary sexual characters and increased later to induce puberty. Discussion: Early diagnosis and treatment play a crucial role in physical and psychological development. We need to continuously monitor the patient as possibility of gonadal axis reversal can occur. Conclusion: This is the youngest case of IHH reported in literature till date. Early identification and treatment of IHH have improved outcomes according to various studies, but compliance to treatment and constant surveillance are of utmost importance.