Removal of protein from plant polysaccharide extract is often regarded as essential step for antioxidant activity evaluation. The aim of this study was to compare two different methods (neutral protease and Sevag) for efficient removal of protein from Lentinus edodes stipe polysaccharide extract. Orthogonal test was used to optimize the parameters of neutral protease deproteinization effects on polysaccharide extracted from Lentinus edodes stipe. Furthermore, antioxidant activity was also investigated by the two deproteinization methods. Results showed that the optimum parameters of deproteinization by neutral protease were pH of 6, temperature of 60 °C, time of 1 h, and enzyme amount 0.2%. Under these conditions, the polysaccharide retention rate was 92.29%, and the deproteinization rate was 84.30%. This result was higher than that of Sevag, which deproteinization rate and polysaccharide retention rate were 55.43% and 82.29%, respectively. The antioxidant activity of polysaccharide declined after the polysaccharide deproteinized for both techniques, however, the polysaccharide deproteinized by Sevag showed the lowest antioxidant activity. Therefore, neutral protease could be used for deproteinization of polysaccharide extracted from Lentinus edodes stipe.