Our aim is to estimate the self-reported one-year prevalence of neck pain in military helicopter pilots and to compare work-related, individual, and health-related factors in the pilots with (neck pain group) and without (reference group) regular or continuous neck pain. A questionnaire was completed by 75% (n = 113) of all military helicopter pilots of the Royal Netherlands Air Force and Navy. The reported one-year prevalence of any neck pain was 43%, and 20% for regular or continuous neck pain. Besides some significant differences in individual and health-related factors (also often reported in the general population), flying hours were significantly higher in pilots with neck pain compared to their colleagues without neck pain. The findings in this study suggest that neck pain in military helicopter pilots is a significant occupational problem and may be a consequence of longer exposure to flying.