Exercise is recognized as an effective method of weight management and short-term appetite regulation tool. The effect of different exercise intensities on appetite regulation hormones in healthy overweight participants has not been intensively studied. The aim of this study was to examine the influence of exercise at individual anaerobic threshold (IAT) and maximal fat oxidation (Fatmax) intensities on the nesfatin-1 response and metabolic health biomarkers in overweight men. Nine healthy overweight males (age, 23.1 ± 1.1 years) volunteered in this study in a counterbalanced order. Blood samples were obtained before, immediately after, and following the first 45 min of recovery for measuring plasma variables. There was significant decrease in plasma levels of nesfatin-1 and leptin after exercise at the IAT intensity which remained lower than baseline following 45 min of recovery. However, nesfatin-1 and leptin levels did not change significantly in any time courses of Fatmax intensity (P > 0.09). Plasma interleukin-6 (IL-6) concentration increased during exercise in both intensities (P < 0.05), whereas changes in free fatty acids (FFAs) and epinephrine concentrations were significant only at the IAT. In addition, a significant correlation was found among nesfatin-1 levels with insulin (r = 0.39, P < 0.05) and glucose (r = 0.41, P < 0.05) at basal and in response to exercise. These results indicate that IAT has a greater exercise-induced appetite regulation effect compared with Fat(max). Based on these data, the intensity of exercise may have an important role in changes of nesfatin-1, leptin, FFA, and epinephrine concentrations even though this was not the case for IL-6 and insulin resistance.