A method of manufacturing a resin multilayer substrate is provided in which a component (3) is incorporated in a stacked body obtained by stacking a plurality of thermoplastic resin sheets (2). The method includes the steps of: softening a first resin sheet (2a) by heating, and pressing the component (3) against the first resin sheet (2a), thereby fixing the component (3) to the first resin sheet (2a); stacking the first resin sheet (2a) on a second resin sheet (2b) having a through hole (14) receiving the component (3) and a third resin sheet (2c) located adjacent to a lower side of the component (3) such that the component (3) is inserted into the through hole (14) and the lower surface of the component (3) faces the third resin sheet (2c); and performing compression bonding by heating and pressurizing the stacked body including these resin sheets (2).