Computed tomography (CT)-measured psoas muscle thickness standardized for height (PMTH) has emerged as a promising predictor of mortality. The study aimed to investigate whether PMTH could accurately predict mortality in patients undergoing hemodialysis. We examined 207 patients (mean age: 63.1 years; men: 66.2%) undergoing hemodialysis for more than 6 months in hospital affiliated clinic. PMTH was calculated at the L3 vertebra level using CT. Patients were divided according to the PMTH cut-off points: 8.44 mm/m in women and 8.85 mm/m in men; thereafter, they were combined into low and high PMTH groups. PMTH was independently correlated with the simplified creatinine index (β = 0.213, P = 0.021) and geriatric nutritional risk index (β = 0.295, P < 0.0001) in multivariate regression analysis. During a median follow-up of 3.7 (1.8–6.4) years, 76 patients died, including 41 from cardiovascular causes. In the multivariate Cox regression analysis, low PMTH (adjusted hazard ratio, 2.48; 95% confidence interval, 1.36–4.70) was independently associated with an increased risk of all-cause mortality. The addition of binary PMTH groups to the baseline risk model tended to improve net reclassification improvement (0.460, p = 0.060). In conclusion, PMTH may be an indicator of protein energy wasting and a useful tool for predicting mortality in patients undergoing hemodialysis.