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Secondary functional hypothalamic amenorrhea (SFHA) is common among female athletes, especially in weight-sensitive sports. The aim of this study was to investigate the link between SFHA and neuromuscular performance in elite endurance athletes.Sixteen eumenorrheic (EUM) and 14 SFHA athletes from national teams and competitive clubs participated. Methods included gynecological examination, body composition (dual-energy x-ray absorptiometry), resting metabolic rate and work efficiency, exercise capacity, knee muscular strength (KMS) and knee muscular endurance (KME), reaction time (RT), blood sampling performed on the third to fifth days of the menstrual cycle, and 7-d assessment of energy availability.SFHA athletes had lower estrogen (0.12 ± 0.03 vs 0.17 ± 0.09 nmol·L−1, P < 0.05), triiodothyronine (T3) (1.4 ± 0.2 vs 1.7 ± 0.3 nmol·L−1, P < 0.01), and blood glucose (3.8 ± 0.3 vs 4.4 ± 0.3 mmol·L−1, P < 0.001) but higher cortisol levels (564 ± 111 vs 400 ± 140 nmol·L−1, P < 0.05) compared with EUM athletes. SFHA had a lower body weight (55.0 ± 5.8 vs 60.6 ± 7.1 kg, P < 0.05), but no difference in exercise capacity between groups was found (56.4 ± 5.8 vs 54.0 ± 6.3 mL O2·min−1·kg−1). RT was 7% longer, and KMS and KME were 11% and 20% lower compared with EUM athletes. RT was negatively associated with glucose (r = −0.40, P < 0.05), T3 (r = −0.37, P < 0.05), and estrogen (r = −0.43, P < 0.05), but positively associated with cortisol (r = 0.38, P < 0.05). KMS and KME correlated with fat-free mass in the tested leg (FFMleg; r = 0.52, P < 0.001; r = 0.58, P < 0.001) but were negatively associated with cortisol (r = −0.42, P < 0.05; r = −0.59, P < 0.001). FFMleg explained the differences in KMS, while reproductive function and FFMleg independently explained the variability in KME.We found lower neuromuscular performance among SFHA compared with EUM athletes linked to a lower FFMleg, glucose, estrogen, T3, and elevated cortisol levels.