Nearly 50% of women with functional hypothalamic amenorrhea (FHA) reveal polycystic ovarian morphology (PCOM), a known risk factor for ovarian hyperstimulation syndrome. However, gonadotropin releasing hormone-agonist (GnRH-a) triggers are not recommended in FHA, since an inadequate endogenous surge in luteinizing hormone (LH) is expected. We aimed to challenge this concept and evaluated LH levels after GnRH stimulation in FHA-women with and without PCOM. In a retrospective cohort study, 82 women with FHA, who underwent a GnRH stimulation test, were included. Thirty-five women revealed PCOM (42.7%). Twenty minutes after GnRH stimulation, there was an increase of serum LH levels in FHA-PCOM (median basal: 2.7 mIU/mL, IQR 1.1-4.6 versus median stimulated: 13.5 mIU/mL, IQR 7.8-21.6, p < 0.001) and in FHA-nonPCOM patients (median basal: 2.5 mIU/mL, IQR 0.5-3.9 versus median stimulated: 5.7 mIU/mL, IQR 2.4-13.9, p < 0.001). Overall, positive correlations (p < 0.001) were found between basal and stimulated LH levels. In FHA-PCOM patients, 42.9% of patients revealed stimulated LH levels >15 mIU/mL, while this was the case in 19.1% of FHA-nonPCOM patients (p = 0.034). In women with FHA-PCOM, ovulation induction with a GnRH-a trigger might be feasible. Future research should focus on the prediction of an adequate response to GnRH triggers in the IVF setting.