Provided is a method of manufacturing a membrane electrode assembly in which an electrode catalyst layer is formed on a surface of an electrolyte membrane. This method includes: a drying of drying a substrate sheet to which a catalyst ink is applied, the catalyst ink containing catalyst support particles on which a catalytic metal is supported, a solvent, and an ionomer; and a heat treatment of performing a heat treatment on the substrate sheet, on which the catalyst ink is dried, after the drying at a heat treatment temperature which is equal to or higher than a glass transition temperature of the ionomer to prepare the electrode catalyst layer. The heat treatment is performed after a concentration of a solvent gas obtained by gasification of the solvent, which remains in a chamber of a heating device for performing the heat treatment, is a predetermined concentration threshold or lower.