Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects nearly one-fourth of the world population and is closely linked to obesity, metabolic syndrome, and poor diet. We conducted a systematic review and meta-analysis to evaluate the impact of exercise on key clinical outcomes in MASLD patients. Methods: A systematic literature search was conducted until 202 September 5, to identify randomized controlled trials (RCTs), post-hoc analyses, and quasi-experimental designs comparing exercise versus standard therapy in MASLD. A random-effects model pooled data as mean differences (MD) or risk ratios (RR) with 95% confidence intervals (CI). Analyses were conducted using R (version 4.5.1). Results: Our meta-analysis included 21 RCTs, 4 post-hoc analyses, and 1 quasi-experimental study (1124 patients; mean age 52.24 ± 7.24 years). Exercise reduced BMI (MD −0.82), serum cholesterol (MD −14.31), ALT (MD −6.56), AST (MD −5.32), FIB-4 (MD −0.19), and NAFLD fibrosis score (MD −0.59), and increased HDL (MD 4.36) versus standard therapy. Weight (MD −2.11) and HOMA-IR (MD −0.59) were not significantly different. Meta-regression showed age increased HOMA-IR (estimate 0.032) and higher BMI reduced HDL (estimate −0.71). Conclusions: Exercise significantly improves key clinical outcomes in MASLD, including BMI, cholesterol, liver enzymes, and fibrosis markers, supporting physical activity as a core component of MASLD management.