Physical exercise improves liver and body composition markers in metabolic dysfunction–associated fatty liver disease (MASLD), but its effects on cerebral hemodynamics and cognitive function in patients with MASLD remain unexplored. We aimed to evaluate the effect of a monitored 16-week exercise intervention on cerebral hemodynamics and cognitive function in patients with MASLD. In this randomized clinical trial, 40 obese patients with MASLD were randomized to either a control group (n=20) on a caloric restriction diet, or an intervention group (n=20) receiving diet plus exercise. The exercise intervention consisted of gradual increases in daily steps and resistance training. Both groups also received monthly classic literature readings to ensure comparable cognitive engagement throughout the study. Transcranial Doppler ultrasound and neurocognitive tests were assessed as primary outcomes. Secondary outcomes included body composition and liver disease parameters. Participants were 60% female, with a mean age of 47±8 years. Intervention adherence was >80%. Daily steps doubled in the intervention group (from 5178 to 10,161; p <0.001) with no changes in controls. The intervention group showed an 8.4% reduction in peripheral arterial stiffness ( p =0.002), 10.4% reduction in resistance index ( p <0.001), and 19.2% decrease in pulsatility index ( p <0.001) with no significant changes in controls. Cognitive function improved in the intervention group, with a 5.9% increase in MoCA score ( p =0.005) and 6.6% increase in Addenbrooke score ( p <0.001). Both groups showed a significant reduction in BMI and body fat percentage (−5.2% and 10.5% intervention, vs. −2.7% and 3.8% in controls). A structured, monitored exercise program improves cerebral hemodynamics, arterial stiffness, and cognitive function in patients with MASLD (NCT05520697).