Background: Oral nutritional supplementation (ONS) with or without exercise (EX) could improve muscle mass (MM) in chronic kidney disease. Methods: Patients were randomized into two groups: (1) ONS and (2) ONS + EX. Thigh muscle area (cm2) and intramuscular lipid content via attenuation were evaluated at baseline and 6 months with computed tomography (CT) to measure MM quantity and quality. Physical function was measured by six-minute walk test (6 MWT), gait speed, handgrip strength (HGS), and Time Up and Go test (TUG) at baseline and 3 and 6 months. Results: The ONS group (n= 14) showed statistically significant improvement in gait speed and HGS; ONS + EX group (n = 10) showed differences in gait speed, in 6 MWT, and HGS. In the ANOVA (3 times × 2 groups), no differences were observed between groups. Greater effect sizes in favor to ONS + EX group were observed in the 6 MWT (d = 1.02) and TUG test (d = 0.63). Muscle quality at six months revealed a significant trend in favor of the EX-group (p = 0.054). Conclusions: Both groups had improved physical function, and greater effect sizes were seen in the ONS + EX group for the 6 MWT and TUG test. Neither MM quantity or quality was improved in either group.