Methylene blue (MB) is one of the most common organic dyes that contaminates textile wastewater. Since it has many adverse effects on human health when exposed at higher doses than recommended limits, MB in effluents must be treated prior to discharge. In this study, the removal of MB from water using electrochemical reactor with flexible graphite electrodes which are low cost, high conductive and stable material as electrode was studied extensively. The effects of operating conditions such as initial concentration of MB, initial solution pH, electrolyte dose, electrical potential, and operating time were investigated to determine optimum conditions. Box-Behnken experimental design (BBD) was performed to optimize the performance of the system with the minimum number of experiments, and to assess influence of the variables on removal efficiency, energy consumption, operating cost and effluent MB concentration. There was a significantly positive effect of electrical potential and electrolyte concentration on MB removal efficiency. In addition, MB removal efficiency increased with the increasing operating time while the MB removal efficiency decreased with increasing initial MB concentration and initial pH. The combined effects of operating time-electrical potential and electrical potential-electrolyte concentration have a positive effect on MB removal efficiency, while the other combined interaction of operating variables didn‘t have a considerable effect on removal efficiency. The highest removal efficiency and lowest operating cost were found to be 99.9% and 0.012 $ m-3 when operating time of 30 min, initial pH of 4, initial MB concentration of 26.5 mg L-1, electrolyte concentration of 0.6 g L-1, and electrical potential of 3V. As a result, process outputs can be predicted thanks to the mathematical model by BBD without experiments, which provides a promising convenience for applicability in real textile wastewater containing methylene blue.