The present invention is to provide a method for refining hydrogen with a hydrogen refining device in which the inside of a cell is divided into a primary side space and a secondary side space by palladium alloy capillaries each having one end being closed and a tube sheet supporting the open end of the palladium alloy capillaries, in which impurity-containing hydrogen is introduced from the primary side space to allow hydrogen to permeate the palladium alloy capillaries so as to collect pure hydrogen from the secondary side space. The method for refining hydrogen has a capability of decreasing the removed amount of gas containing impurities and efficiently collecting pure hydrogen from the secondary side space. From hydrogen with 1000 ppm or less of impurities as raw material hydrogen, gas containing impurities that does not penetrate the palladium alloy capillaries is removed from the primary side space at the flow rate of 10% or less of the introduction flow rate of the raw material hydrogen. Furthermore, gas containing impurities that does not penetrate the palladium alloy capillaries is removed from the primary side space at a flow rate based on the content of impurities contained in raw material hydrogen.