[Problem] A method for manufacturing a packaged medical device, which is capable of hermetically packaging a medical device in a low-oxygen atmosphere and also temporarily raising the oxygen concentration without requiring time management, is provided. [Means for Resolution] This method for manufacturing a packaged medical device includes a sealing step of preparing a packaging bag 20 having a first sub-chamber 21 and a second sub-chamber 22 that are separated from each other, the first sub-chamber 21 being caused to contain a medical device 10 and a deoxygenating agent 25 and then being sealed, and the second sub-chamber 22 being sealed in a higher oxygen concentration than that in the first sub-chamber 21, a communication step of causing the first sub-chamber 21 and the second sub-chamber 22 to communicate with each other, and an irradiation step of irradiating the packaging bag 20 with radiation after the communication step.