A method for manufacturing a packaged medical device includes sealing a packaging bag so that the packaging bag includes a first sub-chamber and a second sub-chamber separated from the first sub-chamber, with the first sub-chamber prevented from communicating with the second sub-chamber. The first sub-chamber contains a medical device and a deoxygenating agent. The first sub-chamber possesses a relatively lower oxygen concentration and the second sub-chamber possesses a relatively higher oxygen concentration. The method also involves communicating the first sub-chamber with the second sub-chamber so that the oxygen concentration in the packaging bag becomes lower than the relatively higher oxygen concentration and higher than the relatively lower oxygen concentration, and irradiating the packaging bag with radiation after the first sub-chamber and the second sub-chamber are in communication with one another.