Decreased skeletal muscle has been identified as a relevant factor for arterial stiffness but has not been thoroughly investigated in peritoneal dialysis (PD) patients. The aim of this study was to investigate the relationship between skeletal muscle and arterial stiffness in PD patients. A cross-sectional study of 658 prevalent PD patients with a mean brachial-ankle pulse wave velocity (baPWV) of 1714 (±501) cm/s and mean skeletal muscle mass of 26.6 (±5.4) kg was performed. Skeletal muscle mass level was significantly higher in males than in females. When examining skeletal muscle mass as a continuous variable, skeletal muscle mass was significantly associated with baPWV in fully adjusted linear regression models in total patients [standardized coefficients (β), -0.181; 95% confidence interval (95% CI), -0.276 to -0.056; P = 0.003] or female patients (β, -0.119; 95% CI, -0.350 to -0.015; P = 0.03) but not in male patients (β, -0.117; 95% CI, -0.300 to 0.011; P = 0.07). Furthermore, in females, a significant association between the middle or highest tertile of skeletal muscle mass and baPWV was found in fully adjusted models (β, -0.123; 95% CI, -0.204 to -0.008; P = 0.03; β, -0.140; 95% CI, -0.228 to -0.016; P = 0.02, respectively). In conclusion, decreased skeletal muscle mass was independently associated with increased baPWV in PD patients, and this association was significant in females but not in males.