Every year, during the processing of agricultural products and food production, many waste materials and by-products are produced. Most of these by-products have bioactive properties, such as antioxidants, which can be extracted to produce products with bioactive properties. In the present study, flaxseed meal, which is obtained as a byproduct of the oil extraction process from flaxseed, was hydrolyzed using two enzymes, trypsin, and pancreatin, with time (15-210 minutes) and enzyme-to-substrate ratio (1-3%) variables. The effect of microwave pretreatment on the antioxidant properties of hydrolyzed protein was investigated by the response surface methodology. Treatment of hydrolyzed protein with trypsin and microwave pretreatment in optimal hydrolysis conditions of 84.02 minutes and enzyme to substrate ratio1.77%, as the optimal treatment with the most antioxidant properties (total antioxidant activity 0.745 (absorbance at 695 nm), DPPH radical scavenging activity of 71.35% and 76.12% Fe chelating activity) were selected. As a result, flaxseed protein hydrolysate, a bioactive product with antioxidant properties, can be used as a natural antioxidant in producing health products and nutritional supplements for athletes.