The aim of this study was to investigate the metabolic and inflammatory fluctuations in two seasonal phases of badminton training, and the ability of youth badminton athletes to respond to an inflammatory challenge given by acute exercise on these markers. Thirteen youth badminton athletes who participated in national and international competitions were recruited. Metabolic and cytokine profile were measured at rest and in response to a maximal exercise intermittent test, in the pre- and final phases of a badminton annual season. At rest, glucose (–7.58 mg/dL; p = 0.045) and HDL-cholesterol (HDL-c) (–26.87 mg/dL; p < 0.0001) decreased at final-season. The variation of HDL-c in response to a maximal exercise test increased at final-season in comparison to pre-season (+ 10.20 mg/dL p = 0.042). Similarly, delta changes of IL-10 (+ 3.41 pg/ml; p = 0.047) and IL-1Ra (+ 141.3 pg/ml; p = 0.031) were greater at final-season. In addition, a significantly greater variation of the anti-inflammatory IL-10/IL-17 ratio was observed at final-season (+ 0.37; p = 0.010). In conclusion, our results showed a major responsivity of IL-10 and IL-1Ra to a maximal exercise even at the end of an entire season. The major responsivity of these cytokines at this time point suggests a more effective acute inflammatory response in youth badminton athletes. Therefore, the results of this study may be applied by coaches, trainers and sport nutritionist for proper training management.