Flying on fighter aircraft is the only human activity that exposes the body to acceleration levels for long periods of time. In this sense, the regular exposure to G forces has been related to a high incidence of flight-related neck pain. The aim is to evaluate flight pilots of the Spanish Air Force (instructors vs. students) diagnosed with flight-related neck pain from a biopsychosocial perspective. Eighteen fighter pilots with flight-related neck pain were divided into two groups: instructor fighter pilots (n = 7) and student fighter pilots (n = 11). The Neck Disability Index (NDI), Cervical Range of Motion (CRoM), Pain Pressure Threshold (PPT), cervical repositioning error, and myoelectric activity were evaluated. Cervical flexion, extension and left and right rotation showed a reduced range of motion in both groups with respect to the normative values of the healthy population. There were no statistically significant differences between the groups (p ≥ 05). The correlational analysis showed a strong association between the NDI and CRoM of the left rotation (β =−0.880, p = 0.002). The NDI also had a positive association with the pilot’s age (β = 1.353, p < 0.01) and the number of flight hours (β = 0.805, p = 0.003). In conclusion, the Cervical Range of Motion at the left rotation seems to determine the perceived degree of disability in both the instructors and students. This factor could be influenced by the number of flight hours and accumulated experience as an F-5 fighter pilot.