BACKGROUND Flight-induced neck pain at high Gz loads or during sustained rotary-wing missions may be caused by limitations in neck muscle function. A better understanding of the contributing factors of excessive external load and internal neck-stabilizing mechanisms would improve the ability to prevent and treat such pain. The aim of this single-blinded cross-sectional study was to evaluate neck neuromuscular function in fighter and helicopter pilots who suffered from frequent neck pain. METHODS Subjects with pain were 16 fighter pilots (FP-P) and 15 helicopter pilots (HP-P) with frequent neck pain episodes who were compared with pain-free controls (FP-C and HP-C). In all groups, neck extensor and flexor muscles were studied by measuring 1) the strength of maximum voluntary contraction (MVC), and 2) fatigue due to a submaximal isometric contraction. The decline (slope) of the electromyogram (EMG) median frequency power spectra was used as an index of fatigue, while initial median frequency (fi) was taken from the intercept of the regression line. RESULTS Two-way analysis of variance (ANOVA) revealed interaction effects for extensor MVC. Post hoc testing showed that FP-P had significantly lower extensor MVC (p = 0.03) than FP-C, while there was no such difference for the HP-P vs. HP-C or between the two control groups. There were no significant effects for MVC-balance (flexors/extensors); nor were there any fi or extensor EMG-slope effects. However, there were interaction effects for flexor EMG-slopes: HP-P showed lower slopes than did HP-C (p = 0.02). CONCLUSIONS To protect and stabilize the head and neck in high Gz environments, higher neck muscle strength is needed; less muscle strength in FP-P may cause further pain and perhaps reduced mission effectiveness. Less localized steep slopes for HP-P might reflect impaired muscle functioning. Specific preventive and clinical attention may be warranted for different types of pilot.