Objective: Obesity is associated with an exacerbated metabolic condition that is related to impaired secretion of hepatokines. This study aimed to compare the effects of 12 weeks continuous aerobic, Tabata, and high intensity interval training (HIIT) on the levels of fetuin-A, fetuin-B, fibroblast growth factor 21 (FGF-21), plasminogen activator inhibitor-1 (PAI-1), fibrinogen-like protein 1 (FGL1), and selenoprotein P. Methods: 44 obese males were randomly divided into four groups (n=11): control group (CT), endurance training group (ET), Tabata group (Tabata), and HIIT group (HIIT). Exercise training programs lasted for 12 weeks/ three sessions per week. Each session lasted 60 minutes, containing warm-up (10 minutes), main training for each group (40 minutes), andending with cooling down (10 minutes). Measurements were made12 and 48 h before the initiation of the main interventional protocols, and then again 48 h after the final session of the training protocol. Results: Baseline data were similar in all groups (p>0.05). There was a significant group-bytime interaction for fetuin B (p=0.0004), FGF-21 (p=0.007), FGL-1 (p=0.0139), weight (p=0.0110), BMI (p=0.009), %fat (p<0.0001) and selenoprotein-1 (p=0.0052). There was a main effect of time for fetuin A and PAI-1 (p<0.0001). The reductions in fetuin B were greater in HIIT vs. CT (mean diff: -0.13) and Tabata vs. CG (mean diff: -0.14) (p<0.05), while decreases in FGF-21 were greater in ET vs. CT (mean diff: -19.1), HIIT vs. CT (mean diff: -26.22)(p<0.05), and Tabata vs. CT (mean diff: -22.8). Reductions in FGL-1 were greater in ET vs. CT (mean diff: -11.5)(p<0.05), HIIT vs. CT (mean diff: -8.1), and Tabata vs. CT (mean diff: - 11.3)(p<0.05). Conclusion: Performing 12 weeks of physical activity led to decreases in weight, BMI, %fat, fetuin-B, FGF-21, FGL-1, and selenoprotein P, and greater reduction observed in the Tabata and the HIIT groups.