Background Exercise is an effective strategy for reducing total and cardiovascular mortality in patients with coronary artery disease. However, it is not clear which modality is best. We performed a meta-analysis to investigate the effects of high-intensity interval versus moderate-intensity continuous training of coronary artery disease patients. Methods We searched MEDLINE, PEDro, LILACS, SciELO and the Cochrane Library (from the earliest date available to November 2016) for controlled trials that evaluated the effects of high-intensity interval versus moderate-intensity continuous training for coronary artery disease patients. Weighted mean differences and 95% confidence intervals were calculated, and heterogeneity was assessed using the I2 test. Results Twelve studies met the study criteria, including 609 patients. High-intensity interval training resulted in improvement in peak oxygen uptake weighted mean difference (1.3 ml/kg/min, 95% confidence interval: 0.6-1.9, n = 594) compared with moderate-intensity continuous training. No significant difference in physical, emotional, and social domain of quality of life was found for participants for participants in the high-intensity interval training group compared with the moderate-intensity continuous training group. Sub-analysis of three studies with isocaloric exercise training showed no significant difference in peak oxygen uptake weighted mean difference (0.4 ml/kg/min, 95% confidence interval: -0.1-0.9, n = 137) for participants in the high-intensity interval training group compared with moderate-intensity continuous training group. Conclusions High-intensity interval training may improve peak oxygen uptake and should be considered as a component of care of coronary artery disease patients. However, this superiority disappeared when isocaloric protocol is compared.