Hormon therapy of the female Kallmann’s Syndrome patient in the setting of a pulmonary embolism presents a challenge. A female with hypogonadotropic hypogonadism is usually presented with two treatment options - combined gonadal hormone replacement or pulsatile gonadotropin releasing hormone. When a patient incurs a contraindication to hormonal therapy, the management of their endocrine disorder becomes much more challenging. Providers and patients must consider the advantages and disadvantages to each treatment option, including the possibility of not treating at all. Given the lack of literature on this rare combination of events, herein we review Kallmann’s Syndrome and its therapeutic options, as well as the hypercoagulability associated with hormone therapy to guide our decision-making process in a true case scenario.