Endothelial dysfunction is associated with increased cardiovascular risk and death in heart transplant recipients (HTx). Although the measurement of peripheral endothelial function is considered a significant predictor of cardiovascular events in several populations, few studies have investigated this outcome after therapeutic strategies, including different exercise types, duration, and intensity. This systematic review and meta-analysis aimed to investigate the effects of continuous moderate exercise (CON) or high-intensity interval training (HIIT) to improve endothelial function (EF) in HTx. The search was conducted in Cochrane Central Registry of Controlled Trials (CENTRAL), MEDLINE (via PubMed), Web of Science and Scopus/Elsevier, CINAHL/Ebsco, Physiotherapy Evidence Database (PEDro), LILACS/BIREME, and SciELO databases. Quality of the evidence was assessed using the Grading of Recommendations Assessment Development and Evaluation (GRADE). The search strategy retrieved 5192 titles. A total of four articles met the inclusion criteria and were included for the qualitative analysis. Meta-analysis showed that exercises improved EF ([mean difference-MD] 3.48 95% CI - 0.29 to 7.25, p = 0.007) when compared with the control. However, there was a poor quality of evidence to demonstrate that CON or HIIT is better than usual care to improve EF. Exercise training provides benefits to patients, but the poor quality of evidence does not allow us to state that exercise is related to endothelial function improvement in HTx.