To provide a method for manufacturing a flow path device internally provided with a flow path for allowing a liquid to flow by compression bonding two or more members to each other, wherein the hydrophilic property of a surface of the flow path can be maintained for a long period of time. A flow path device is manufactured by forming a hydrophilic coating film using a treatment liquid including a hydrophilizing agent in at least one member of the members, the coating film covering a surface of the member at a side to be joined to another member, then irradiating only a joining surface of the hydrophilic coating film with ultraviolet rays or plasma derived from an oxygen-containing gas in the member having the hydrophilic coating film, and irradiating at least the joining surface with ultraviolet rays or plasma derived from an oxygen-containing gas in a member having no hydrophilic coating film, and compression bonding the two or more members having been subjected to such treatment.