We performed a systematic review and meta-analysis of randomized controlled trials (RCTs) to assess the effects of magnesium (Mg) supplementation on the lipid profile in type 2 diabetes (T2DM) patients. Web of Science, Scopus, PubMed, and Embase databases were searched to infinity until 30 January 2020. Weighted mean differences (WMD) were pooled using a random-effects model. Heterogeneity, sensitivity analysis, and publication bias were reported using standard methods. The pooled analysis of 12 randomized controlled trial s indicated that Mg administration led to significant reduction of serum low-density lipoprotein (LDL) levels (p = 0.006). However, our results revealed that Mg supplementation did not have any effect on triglycerides (TG), total cholesterol (TC), and high-density lipoprotein (HDL) serum concentrations among T2DM patients in comparison with the control group. Subgroup analysis based on duration of study suggested that more than 12 weeks of Mg supplementation significantly decreased the serum TC levels (p = 0.002). Subgroup analysis comparing the dose of intervention indicated that Mg supplementation less than 300 mg significantly decreased the serum LDL concentrations (p < 0.001), while more than 300 mg of Mg supplementation significantly increased the serum HDL levels (p = 0.026). In a subgroup analysis comparing the type of intervention, it displayed that inorganic Mg supplementation decreased the LDL (p < 0.001) and TC (p = 0.003) levels, while organic Mg supplementation showed no difference. Mg supplementation has a beneficial effect on lowering LDL level in T2DM patients. However, we have to note that any research performed so far is not sufficient for making robust guidelines to use Mg supplementation in clinical practice.