Chronic kidney disease (CKD) leads to gradual muscle mass loss, which is strongly associated with lower functional capacity, which limits a patient’s daily activities. The aim of the present study is to examine the effects of a 4-month intradialytic exercise program on the functional capacity and body composition of kidney transplant (KT) candidates. Twenty-nine male patients on hemodialysis (HD) waiting for a kidney transplant, with a mean age of 53.86 ± 9.56 years old and BMI 27.11 ± 5.55 kg/m2, were randomly assigned into the following two groups: A (nA = 15 HD patients), who followed a 4-month intradialytic exercise program combining aerobic and resistance training, with a supervised, progressively increasing workload, and B (nB = 14 HD patients), who continued to receive usual care. At baseline and the end of the study, the KT candidates underwent a 6-min walking distance (6-MWD), and a 10-repetition sit-to-stand test (10-STS) to access physical function, a handgrip strength (HGS) test to evaluate the muscle strength of the non-fistula hand. Moreover, the bioelectrical impedance analysis (BIA) was performed to assess body composition indices, such as body fat (BF), body fat mass index (BFMI), fat-free mass index (FFMI), body cell mass (BCM), basal metabolic rate (BMR), extracellular water (ECW), intracellular water (ICW), total body water (TBW) and phase angle (PhA). Following the exercise program, group A showed favorable improvements in HGS (from 26.59 ± 9.23 to 28.61 ± 9.58 kg, p < 0.05) and 6-MWD (from 427.07 ± 7.66 to 468.16 ± 11.39 m, p < 0.05). Intergroup results from 6-MWD showed a statistically significant difference (Δp = 0.04), at the end of the study. Moreover, group A results from BIA revealed a significant increase of BMR by 2.4% (p < 0.05), ECW by 3.6% (p = 0.01), ICW by 3.8% (p = 0.01), TBW by 4.1% (p = 0.01), lean mass by 2.7% (p = 0.01), and PhA by 13.3% (p = 0.04), while a reduction in BF by 5.0% (p = 0.01) and BFMI by 6.6% (p = 0.03) was also noticed. At the end of the study, group A showed statistical differences in BMR (Δp = 0.01), BMR/BW (Δp = 0.01), dry lean (Δp = 0.01), and PhA (Δp = 0.03), compared to the group B. Linear regression analysis in group A after training showed positive correlations between HGS and both PhA (r = 0.52, p = 0.04) and FFMI (r = 0.64, p = 0.01), and a strong negative correlation between 6-MWT and BF (r = −0.61, p = 0.01). In conclusion, a 4-month intradialytic exercise program can enhance body composition and some physical parameters in HD patients awaiting kidney transplantation.