Heart Transplant (HTx) is the ultimate chance of life for end stage Heart Failure (HF). Exercise training has consistently shown the potential to improve functional capacity in various chronic heart diseases. Still, the evidence in HTx recipients is scarcer. This study aims to systematically review the literature to evaluate the effectiveness and safety of Exercise-based Cardiac Rehabilitation (EBCR) in HTx recipients and to identify possible moderators of success. We conducted a systematic review and meta-analysis of randomized controlled trials on the effect and safety of EBCR in adult HTx recipients. The primary outcome was functional capacity, measured by Peak Oxygen Uptake (pVO2). We searched CENTRAL, MEDLINE, Embase, Scopus, and Web of Knowledge databases until December 2020, reviewed references of relevant articles and contacted experts. Usual care (UC), the different dosages of exercise regimens and alternative settings were allowed as comparators. A quantitative synthesis of evidence was performed using random-effects meta-analyses. A total of 11 studies with 404 patients were included. Nine studies comprising 306 patients compared EBCR with usual care. They showed that EBCR improved pVO2 compared to usual care (Mean Difference [MD] 3.03 mL/kg/min, 95% CI [2.28-3.77]; I 2 = 32%). In the subgroup analysis, including length of intervention and timing of enrollment after HTx, no significant moderator was found. Two trials, with 98 patients total, compared High Intensity Interval Training (HIIT) and Moderate Intensity Continuous Training (MICT). HIIT attained a significant edge over MICT (MD 2.23 mL/kg/min, 95% CI [1.79-2.67]; I 2 = 0%). No major adverse events associated with EBCR were reported. We found moderate quality evidence suggesting EBCR has a significant benefit on functional capacity improvement HTx recipients at the short-term. HIIT showed superiority when compared to MICT. Research focusing long term outcomes and standardized protocols are needed to improve evidence on EBCR effectiveness.