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This study aimed to assess muscle wasting and risk of protein energy wasting (PEW) in hemodialysis (HD) patients using an ultrasound (US) imaging method. PEW was identified using the ISRNM criteria in 351 HD patients. Quadriceps muscle thickness of <i>rectus femoris</i> (RF) and <i>vastus intermedius</i> (VI) muscles and cross-sectional area (CSA) of the RF muscle (RF_CSA) were measured using US and compared with other physical measures. Associations of US indices with PEW were determined by logistic regression. Irrespective of gender, PEW vs. non-PEW patients had smaller RF, VI muscles, and RF_CSA (all <i>p</i> < 0.001). US muscle sites (all <i>p</i> < 0.001) discriminated PEW from non-PEW patients, but the RF_CSA compared to bio-impedance spectroscopy had a greater area under the curve (AUC, 0.686 vs. 0.581), sensitivity (72.8% vs. 65.8%), and specificity (55.6% vs. 53.9%). AUC of the RF_CSA was greatest for PEW risk in men (0.74, 95% CI: 0.66–0.82) and women (0.80, 95% CI: 0.70–0.90) (both <i>p</i> < 0.001). Gender-specific RF_CSA values (men < 6.00 cm²; women < 4.47 cm²) indicated HD patients with smaller RF_CSA were 8 times more likely to have PEW (AOR = 8.63, 95% CI: 4.80–15.50, <i>p</i> < 0.001). The US approach enabled discrimination of muscle wasting in HD patients with PEW. The RF_CSA was identified as the best US site with gender-specific RF_CSA values to associate with PEW risk, suggesting potential diagnostic criteria for muscle wasting.