Introduction: Prediabetes involves impaired glucose regulation and alterations in adipokines. The aim of this study was to investigate the immediate effects of high-intensity interval training (HIIE) and moderate-intensity continuous exercise (MICE) on metabolic function in obese prediabetic individuals. Methods: Eight obese prediabetic men (30-45 years) were assigned to three conditions in a crossover design: HIIE, MICE, and control. The HIIE protocol consisted of 10*1 min bursts at 90-100% HRmax with active rest, and the MICE protocol consisted of 30 minutes of continuous exercise at 60-65% HRmax. Blood samples were collected at four time points (before, immediately, 3h, and 24h after exercise) and serum levels of GDF-15, adiponectin, leptin, and OGTT markers were measured. Results: Results of repeated-measures ANOVA showed that the effect of time on leptin levels was significant (p < 0.05), and both types of exercise resulted in significant decreases compared to the control group (p < 0.05), although no difference was observed between HIIE and MICE (p > 0.05). Serum adiponectin levels increased significantly after MICE compared with baseline and control groups (p < 0.05), whereas no significant changes were observed in HIIE; however, there was no significant difference between the two exercise conditions (p > 0.05). GDF-15 levels increased significantly after both HIIE and MICE training, with no significant difference between the two exercise conditions (p > 0.05). Both HIIE and MICE differently altered the glucose response pattern over time during the OGTT, but the average total glucose did not differ significantly between the two exercise groups (p > 0.05). Conclusion: HIIE and MICE exercises reduced leptin and altered glucose response patterns (at 90 min) in obese prediabetic subjects, without significant differences between them. The type and intensity of exercise regulate metabolism, but more studies are needed.