Introduction Exercise-based cardiac rehabilitation for patients with coronary artery disease (CAD) significantly improves their outcome, although the optimal mode of exercise training remains undetermined. Previous analyses have been constrained by small sample sizes and a limited focus on clinical parameters. Further, results from previous studies have been contradicted by a recently published large RCT. Method We performed a meta-analysis of published randomised controlled trials to compare high intensity interval training (HIIT) and moderate intensity continuous training (MCT) in their ability to improve patients' aerobic exercise capacity (VO2peak) and various cardiovascular risk factors. We included patients with established coronary artery disease without or without impaired ejection fraction. Results Ten studies with 472 patients were included for analyses (218 HIIT, 254 MCT). Overall, HIIT was associated with a more pronounced incremental gain in participants' mean VO2peak when compared with MCT (+1.78 mL/kg/min, 95% CI: 0.45-3.11). Moderate intensity continuous training however was associated with a more marked decline in patients' mean resting heart rate (-1.8/min, 95% CI: 0.71-2.89) and body weight (-0.48 kg, 95% CI: 0.15-0.81). No significant differences were noted in the level of glucose, triglyceride and HDL at the end of exercise program between the two groups. Conclusion High intensity interval training improves the mean VO2peak in patients with CAD more than MCT, although MCT was associated with a more pronounced numerical decline in patients' resting heart rate and body weight. The underlying mechanisms and clinical relevance of these results are uncertain, and remain a potential focus for future studies.