We report a case of a 28-year-old Japanese woman diagnosed with functional hypothalamic amenorrhea (FHA). Although oral estrogen-progestin therapy was initially recommended, laboratory tests revealed an inherited antithrombin (AT) deficiency, which is associated with an increased risk of venous thromboembolism (VTE). To mitigate this risk, we selected Kampo medicine (Japanese traditional herbal medicine) as an alternative treatment for amenorrhea. She was prescribed Keishibukuryogan and Shigyakusan, which led to the resumption of menstruation shortly after initiation. Subsequently, Tokakujokito was added to address persistent constipation, resulting in the regularization of her menstrual cycle and resolution of associated symptoms without adverse effects. This case suggests that Kampo medicine may offer a viable therapeutic alternative for managing menstrual disorders in patients predisposed to thrombosis.