INTRODUCTION: 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. METHODS: Sixteen eumenorrheic (EUM) and 14 SFHA athletes from national teams and competitive clubs participated. Methods included gynecological examination; body composition (DXA);; 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 3rd-5th day of the menstrual cycle, and 7-day assessment of energy availability. RESULTS: SFHA athletes had lower estrogen (0.12 ±0.03 vs. 0.17 ±0.09 nmol/L, p<0.05), triiodothyronine (T3) (1.4 ±0.2 vs. 1.7 ±0.3 nmol/L, p<0.01), and blood glucose (3.8 ±0.3 vs 4.4 ±0.3 mmol/L, p<0.001) but higher cortisol levels (564 ±111 vs. 400 ±140 nmol/L, p<0.05) compared to 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/kg). RT was 7% longer, and KMS and KME were 11% and 20% lower compared to 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 differences in KMS, while reproductive function and FFMleg independently explained the variability in KME. CONCLUSION: We found lower neuromuscular performance among SFHA compared to EUM athletes linked to a lower FFMleg, glucose, estrogen, T3 and elevated cortisol levels.