Background Patients on hemodialysis have less exercise capacity and lower health-related quality of life than healthy individuals without chronic kidney disease (CKD). One of the factors that may influence exercise behavior among these patients is their perception of exercise benefits and barriers. The present study aimed to assess the perception of hemodialysis patients about exercise benefits and barriers and its association with patients’ health-related quality of life. Methods In this cross-sectional study, 227 patients undergoing hemodialysis were randomly selected from two dialysis centers. Data collection was carried out using dialysis patient-perceived exercise benefits and barriers scale (DPEBBS) and kidney disease quality of life short form (KDQOL-SF). Data were analyzed using SPSS software ver. 21. Results The mean score of DPEBBS was 68.2 ± 7.4 (range: 24 to 96) and the mean KDQOL score was 48.9 ± 23.3 (range: 0 to 100). Data analysis by Pearson correlation coefficient showed a positive and significant relationship between the mean scores of DPEBBS and the total score of KDQOL (r = 0.55, p < 0.001). Moreover, there was a positive relationship between the mean scores of DPEBBS and the mean score of all domains of KDQOL. Conclusion Although most of the patients undergoing hemodialysis had a positive perception of the exercise, the majority of them do not engage in exercise; it could be contributed to the barriers of exercise such as tiredness, muscle fatigue, and fear of arteriovenous fistula injury. Providing exercise facilities, encouraging the patients by the health care provider to engage in exercise programs, and incorporation of exercise professionals into hemodialysis centers could help the patients to engage in regular exercise.