The USOC and USA Track & Field said Flanagan, who preferred not to have an official ceremony, received her silver medal at her home in Portland, Oregon, earlier on Monday.
"Receiving my proper medal and having the record books changed is a dream come true," Flanagan, said in a statement.
"I greatly appreciate the USOC's efforts to host a more formal medal ceremony in my honour, but with my coach and my family, I have decided to forego that option and instead celebrate in private.
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"This news, and receiving my medal, are all that I need to feel incredibly fulfilled and happy."
The 2008 bronze medal previously owned by Flanagan, 36, has been returned to the IOC.
(Reporting by Frank Pingue in Toronto, editing by Pritha Sarkar)
