We examined the effects of six weeks of dark chocolate supplementation combined with interval jump rope exercise (JRE) on inflammatory cytokines, adipokines, and body composition in obese adolescent boys. Forty-eight obese adolescent boys (age = 15.4 ± 1.1 years and body mass index = 32.2 ± 2.4 kg/m2) were randomly assigned into one of four groups: JRE + white chocolate (JW; n = 13), JRE + dark chocolate supplementation (JD; n = 13), dark chocolate supplementation (DS; n = 12), or control (C; n = 12). Participants in JW and JD groups performed JRE for three times per week for six weeks. Participants in the DS and JD groups consumed 30 g of dark chocolate containing 83% of cocoa. Body composition, pro-inflammatory cytokines ((hs-CRP, TNF-α, IL-6), adipokines (leptin, resistin, RBP-4, chemerin, MCP-1), and anti-inflammatory adipokines (irisin, adiponectin)) were evaluated prior to and after the intervention trials. All three intervention trials significantly (p < 0.05) decreased body mass, waist-hip ratio, fat mass, hs-CRP, TNF-α, IL-6, leptin, resistin, RBP-4, and MCP-1, and increased irisin and adiponectin concentrations. The improvements in these parameters were greater in the JD group, and additionally, chemerin concentrations decreased only in the JD group. JD enhanced adiponectin concentrations and decreased IL-6 concentrations compared to C. Moreover, JD significantly reduced chemerin concentrations, an effect not observed in any of the other interventions. We demonstrated that dark chocolate supplementation potentiated JRE-induced decreases in body mass, WHR, FM, hs-CRP, TNF-α, IL-6, leptin, resistin, RBP-4, and MCP-1, chemerin as well as increases irisin and adiponectin concentrations in obese adolescent boys. Therefore, JRE combined with dark chocolate supplementation could be a beneficial in reducing obesity-induced inflammation in adolescent boys.