Performance of a three-module membrane column in high gas purification processes to remove highly permeable impurities has been experimentally evaluated using the separation of the CH4/CO2 binary gas mixture (CO2 content of 1 vol %) as an example. The time to reach the steady-state regime in a total reflux operating mode has been determined for two configurations, the three-module membrane column (TMC) and the continuous membrane column (CMC) proposed by Hwang with colleagues. The influence of the efficiency of removal of the highly permeable impurity on the degree of purification of the low-permeability target component has been shown. The obtained product purity has appeared to be 99.997 or 99.93% at the recovery rate of 15 or 81%, respectively. It has been demonstrated that the three-module membrane column hold promise for use in high gas purification.