Introduction High-intensity interval training (HIIT) is considered a time-efficient strategy to improve metabolic health. We performed a systematic meta-analysis to assess the effects of HIIT on inflammatory markers and adipo-cytokines compared with control conditions (CON) or moderate-intensity continuous training (MICT) in individuals with metabolic disorders. Methods Up to January 2020, electronic databases were searched for HIIT interventions based on populations with metabolic disorders including diabetes, metabolic syndrome, polycystic ovary syndrome, non-alcoholic fatty liver disease or overweight/obesity, with outcome measurements that included IL-6, TNF-alpha, CRP, leptin or adiponectin and training >= 2 weeks. Random-effects models were used to aggregate a mean effect size (ES), 95% confidence intervals (Cis), and potential moderators were explored. Results Twenty-nine studies involving 841 participants were included in the meta-analysis. HIIT improved circulating adiponectin (P = .02), leptin (P = .02), and TNF-alpha (P = .003) when compared to CON. There were no differences between groups in IL-6 and CRP. Intervention duration was a significant moderator for the effect of HIIT on IL-6, and leptin (P < .05). Conclusion High-intensity interval training improves circulating TNF-alpha, leptin and adiponectin, thereby indicating that it may be an effective and time-efficient intervention for controlling low-grade inflammation in individuals with metabolic disorders.