We present a patient with treatment refractory short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT) who was found to have low levels of serum testosterone supporting the hypothalamic connection to this trigeminal autonomic cephalalgia. Clomiphene citrate therapy induced a significant elevation of testosterone levels (by its effect on hypothalamic estrogen receptors) and led to a dramatic reduction in SUNCT attacks. Hormonal manipulation may be a treatment strategy for hypothalamic-influenced trigeminal autonomic cephalalgias.