Prediabetes and type 2 Diabetes Mellitus (T2DM) are characterized by increased blood sugar concentration and insulin resistance. Although there are only a few reports of potential benefits of flaxseed’s consumption on different metabolic parameters, there is no evidence of its effect among people with these conditions. The present systematic review and meta-analysis aimed to assess the effect of flaxseed supplementation on glycemic control variables and insulin resistance in prediabetes and T2DM. A literature search was conducted through PubMed, Cochrane Central Register of Controlled Trials (CENTRAL), and Web of Science, to identify Randomized Control Trials (RCTs) that evaluated the effect of milled or ground flaxseed supplementation on fasting blood glucose, HbA1c, insulin concentrations, or HOMA-IR. The data were analyzed using Comprehensive Meta-Analysis (CMA) software version 3.3 in a fixed-effect model. Seven studies were included in the systematic review and the meta-analysis, the results showed a significant reduction on fasting blood sugar (SMD: −0.392, 95% CI: −0.596, −0.187, p = <0.001, I2 = 64.81%) insulin concentrations, (SMD: −0.287, 95% CI: −0.534, −0.041, p = 0.022, I2 = 32.53%), HbA1c (SMD: −0.442, 95% CI: −0.770, −0.114, p = 0.008, I2 = 11.058%), and HOMA-IR (SMD: −0.284, 95% CI: −0.530, −0.038, p = 0.024, I2 = 0.00%) after flaxseed supplementation. Flaxseed supplementation seems to improve glycemic control variables and insulin resistance in prediabetes and T2DM; however, more RCTs are needed to have more decisive evidence about doses, method of supplementation, and the possible effect of synergy with the dietetic treatment. •Flaxseed supplementation may improve glycemic control in prediabetes and type 2 diabetes mellitus.•Flaxseed supplementation may improve insulin concentrations and insulin resistance in prediabetes and type 2 diabetes mellitus.•Further studies are needed to address methodological aspects, such as the administration, dosage, and the combined effect with other treatments.