BACKGROUND This study systematically explores the effects of self-administered physical exercise training on alleviating flight-associated neck pain and improving functional outcomes in military pilots. METHODS PubMed, Cochrane Library, Web of Science, Embase, Scopus, China National Knowledge Infrastructure, and the Chinese biomedical literature service system (SinoMed) were searched from inception to September 18, 2024. Standardized mean differences (SMD) or mean differences (MD) and 95% confidence intervals (95% CI) were calculated and data pooled using fixed or random effects models. RESULTS Included were 7 studies involving 366 patients having neck pain. Military pilots who underwent self-administered physical exercise training showed a significant reduction in their Visual Analog Scale scores (SMD = -0.25, 95% CI: -0.47 to -0.03). The maximum voluntary contraction (MVC) of neck extension and flexion in military pilots did not increase significantly after self-administered physical exercise training (extension MVC, MD = 3.00, 95% CI: -1.33 to 7.33; flexion MVC, MD = 1.12, 95% CI: -2.12 to 4.36). CONCLUSIONS Self-administered physical exercise training is an effective method for alleviating flight-associated neck pain in military pilots. However, its effectiveness in improving neck function among military pilots remains uncertain. Chen H, Wang M, Li J, Wang X, Fu Y, Gao B. Self-administered physical exercise training and flight-associated neck pain in military pilots. Aerosp Med Hum Perform. 2025; 96(4):339-349.