PROBLEM TO BE SOLVED: To provide a method for manufacturing a medical container for preventing a liquid leak caused by the generation of pinholes or the like at a sealing part in the method for manufacturing a medical container of a type for expanding between sheets that are unsealed parts of a peripheral edge part of a medicament chamber to fill a medicament and sealing after the filling.SOLUTION: A method for manufacturing a medical container includes: performing a container body forming process for forming a container body including a peripheral edge sealing part having an unsealed part that is used as a medicament filling port by using a container material made of a soft thermoplastic resin sheet performing a medicament filling process for filling a medicament by using the unsealed parts 25, 35 and performing a filling port sealing process after filling the medicament. In the filling port sealing process, heating press is performed in such a manner that a thickness of a medicament chamber side sealing part 22a of a filling port sealing part 22 is thinner than that of an outer side sealing part 22b of the filling port sealing part.