People with Type 2 diabetes mellitus (T2DM) are reported to have a high prevalence of metabolic syndrome (MetS), which increases their risk of cardiovascular events. Our aim was to determine the effect of physical activity (PA) on metabolic syndrome markers in people with T2DM. The study design was a systematic review and meta-analysis of randomised controlled trials evaluating the effect of PA on MetS in adults with T2DM. Relevant databases including SPORTdiscus, Cochrane Central Register of Controlled Trials, CINAHL, MEDLINE, PsycINFO, EMBASE, SocINDEX were searched up to August 2022. Primary endpoints were changes in MetS markers (blood pressure, triglyceride, high-density lipoprotein, fasting blood sugar, and waist circumference) after an exercise intervention. Using a random effect model with 95% confidence interval (CI), the mean difference between intervention groups and control groups were calculated. Twenty-six articles were included in the review. Overall, aerobic exercise had a significant effect on waist circumference (Mean Difference: −0.34 cm, 95% CI: −0.84, −0.05; effect size: 2.29,I2= 10.78%). The effect sizes on blood pressure, triglyceride, high-density lipoprotein, fasting blood sugar were not statistically significant. No significant differences were found between exercise and control group following resistance training. Our findings suggest that aerobic exercise can improve waist circumference in people with T2DM and MetS. However, both aerobic and resistance exercise produced no significant difference in the remaining MetS markers. Larger and higher-quality studies are required to determine the full effects of PA on MetS markers in this population.