Purpose: To evaluate the effects of physical exercise on neck and shoulder muscle strength and pain in military pilots.Method: Embase, PubMed, and Cochrane Library databases were searched studies published up to April 1, 2022. Studies that met the screening criteria were included in the final meta-analysis. We calculated neck and shoulder maximal voluntary isometric contractions (MVICs), prevalence of pain, and pain intensity. Heterogeneity was explored by subgroup and sensitivity analyses.Result: A total of 15 studies with 907 participants were included. In the exercise group, muscle strength was significantly increased in four directions of neck motion: flexion (standardized mean difference (SMD) = 0.45; 95% CI, 0.08–0.82), extension (SMD = 0.63; 95% CI, 0.27–1.00), right lateral flexion (Rtflx) (SMD = 0.53; 95% CI, 0.12–0.94), and left lateral flexion (Ltflx) (SMD = 0.50; 95% CI, 0.09–0.91). Subgroup analysis showed that fighter pilots, strength plus endurance training, and a follow-up period <20 weeks exhibited more significant muscle strength improvements than helicopter pilots, simple strength training, and a follow-up period ≥20 weeks. Overall, the pooled odds ratio (OR) for the effect of physical exercise on the prevalence of neck pain was not statistically significant (I2 = 60%). Sensitivity analysis revealed that the heterogeneity was restored after removing each of two studies (I2 = 47%), and the pooled OR was statistically significant (OR = 0.46; 95% CI, 0.23 to 0.94, or OR = 0.47; 95% CI, 0.24–0.91). Furthermore, compared with observational studies (OS), the reduction in the prevalence of neck pain was more significant in randomized controlled trials (RCTs) (OR = 0.37; 95% CI, 0.18–0.78). No significant differences in the effects of exercise on shoulder muscle strength and neck and shoulder pain intensity were observed.Conclusion: Physical exercise can improve neck muscle strength in military pilots. After removing studies that may be the source of heterogeneity, exercise showed a protective effect on neck pain, especially in RCTs. The conclusion that exercise had no effects on shoulder muscle strength and pain intensity should be taken with caution.