Non-alcoholic fatty liver disease (NAFLD) and cardiometabolic disorders are highly prevalent in obese individuals. Physical exercise is an important element in obesity and metabolic syndrome (MetS) treatment. However, the vast majority of individuals with obesity do not meet the general physical activity recommendations (i.e. 150 min of moderate activity per week). The present study aimed to investigate the impact of a highly time-saving high-intensity interval training (HIIT) protocol (28 min time requirement per week) on NAFLD fibrosis (NFS) and cardiometabolic risk scores in obese patients with MetS and elevated NFS values. Twenty-nine patients performed HIIT on cycle ergometers (5 x 1 min at an intensity of 80 - 95% maximal heart rate) twice weekly for 12 weeks and were compared to a control group without exercise (CON, n = 17). Nutritional counseling for weight loss was provided to both groups. NFS, cardiometabolic risk indices, MetS z-score, cardiorespiratory fitness (VO2max) and body composition were assessed before and after intervention. The HIIT (-4.3 kg, P < 0.001) and CON (-2.3 kg, P = 0.003) group significantly reduced body weight. There were no significant group differences in relative weight reduction (HIIT: -3.5%, CON: -2.4%). However, only the HIIT group improved NFS (-0.52 units, P = 0.003), MetS z-score (-2.0 units, P < 0.001), glycemic control (HbA1c: -0.20%, P = 0.014) and VO2max (+3.1 mL/kg/min, P < 0.001). Decreases in NFS (-0.50 units, P = 0.025) and MetS z-score (-1.4 units, P = 0.007) and the increment in VO2max (3.3 mL/kg/min, P < 0.001) were significantly larger in the HIIT than in the CON group. In conclusion, only 28 min of HIIT per week can elicit significant improvements in NFS and a several cardiometabolic health indices in obese MetS patients with increased NFS grades. Our results underscore the importance of exercise in NAFLD and MetS treatment and suggest that our low-volume HIIT protocol can be regarded as viable alternative to more time-consuming exercise programs.