Non-alcoholic fatty liver disease (NAFLD), linked to sedentary lifestyles and metabolic dysfunction, is highly prevalent. Exercise is an established intervention, but the relative efficacy of different exercise modalities remains unclear. The aim of this study was to compare the effects of moderate-intensity continuous aerobic training and High-Intensity Interval Training (HIIT) on physical fitness, biochemical parameters, and liver function in NAFLD patients. Sixty NAFLD patients (32 males, 28 females; age: 49.7±8.7 years; BMI: 31.1±3.3 kg/m2) were randomized into HIIT, aerobic training, and control cohorts. The HIIT cohort performed 4-minute high-intensity intervals at 85-95% of peak heart rate, interspersed with 3-minute active recovery at 60-70% of peak heart rate for 30-40 minutes per session. The aerobic training cohort performed continuous exercise at 60-70% of peak heart rate for 45-60 minutes per session. Both intervention cohorts underwent 12 weeks of supervised training, thrice weekly. Before and after the intervention, assessments included cardiorespiratory fitness, muscular strength, flexibility, lipid profile, liver enzymes, inflammatory markers, insulin sensitivity, and oxidative stress markers. Compared to controls, both exercise cohorts showed significant improvements in cardiorespiratory fitness, muscular strength, and flexibility. However, HIIT elicited superior enhancements in cardiorespiratory fitness and muscular strength. Biochemically, both exercise cohorts exhibited reductions in triglycerides, low-density lipoprotein (LDL) cholesterol, liver enzymes (alanine aminotransferase [ALT], aspartate aminotransferase [AST]), inflammatory markers (C-reactive protein [CRP], interleukin-6 [IL-6]), insulin resistance (homeostatic model assessment of insulin resistance [HOMA-IR]), and oxidative stress markers (malondialdehyde [MDA], protein carbonyl). Notably, HIIT yielded more substantial improvements in these parameters. HIIT and traditional aerobic training are effective in improving physical fitness and ameliorating biochemical indicators in NAFLD patients. Notably, HIIT appears to be more advantageous in enhancing cardiorespiratory fitness, muscular strength, and metabolic, inflammatory, and oxidative stress profiles, suggesting its potential as a time-efficient and effective exercise modality for managing NAFLD.