Dialysis patients are less physically active and have lower physical function compared to the general population. In the literature, the most widely used exercise program for hemodialysis patients is cycling during dialysis, whereas added benefit of other exercise modalities remains unknown. This study aimed to determine the effect of adding functional exercise and exercise counseling to the basic exercise program of cycling during dialysis. Forty hemodialysis patients were randomized into an experimental group (n = 20) and an intradialytic cycling control group (n = 20). In the first phase (8 weeks), the experimental group attended a guided functional exercise before the dialysis and continued with a cycling session during dialysis. In the second phase (8 weeks) the experimental group was instructed to exercise at home and continued with the program of intradialytic cycling as did the control group. After 8 weeks, the experimental group showed a significant advancement in 10-repetition-sit-to-stand test (p = 0,021), and maintained it until week 16 (p = 0,037). The experimental group demonstrated significantly better outcomes compared to control group at handgrip strength test (p = 0,004), sit-and-reach test (p < 0,001), Stork balance test (p < 0,001), and at back scratch test (p = 0,003). In week 16, the experimental group retained the performance gains from the first phase. Both groups demonstrated a significant increase in dialysis adequacy (Kt/V) compared to their baseline values (p < 0,05) with no significant between-group differences. Patients with above-median Outcome Expectations for Exercise (OEE) and Decisional Balance (DB) scores (> 3.15 and > 1.3, respectively) expressed significantly better adherence to intradialytic cycling (89% vs. 76%, 89% vs. 77%, respectively, p < 0.05). Experimental group patients with above-median OEE (but not DB) score had significantly better adherence to supervised and home-based functional exercise (93% vs. 81% and 85% vs. 60%, respectively, p < 0.05). Baseline DB score predicted the final result in the hand-grip test and 6-minute walk test. Low OEE and, to a lesser degree, low DB questionnaire scores associate with inferior adherence to dialysis bundled and home-based exercise programs and may help define patient subsets in need of intensified motivational input by exercise caregivers. Our research showed that functional training is practical, feasible, and effective in improving the physical function of HD patients and can successfully prepare patients for independent exercise in the home environment. This study supports the assumption that combined training is more effective compared to solely aerobic intradialytic exercise.