The 25-year-old won mixed doubles gold at the 2008 Games in Beijing and a bronze medal in the men's doubles in London four years later. Another Korean player, Kim Ki-jung, was also banned for one year.
The ban was effective until January 23, 2015, the federation said in a statement, meaning the players would miss the Asian Games in Incheon later this year.
"Korean badminton players Kim Ki-jung and Lee Yong-dae have each received a one-year sanction for violating the requirements relating to filing whereabouts information and resulting missed tests under the BWF Anti-Doping Regulations," the BWF said.
"Kim and Lee were required to provide whereabouts information for the BWF to conduct out-of-competition testing. In 2013, both athletes accumulated three whereabouts failures in connection with this administrative process."
The BWF said it chose not to dish out the maximum two-year ban "due to the Badminton Korea Association's failure ... to make diligent efforts to keep the BWF informed about the players' whereabouts."
A doping hearing panel recommended that the Korean association should be fined and the BWF said it would determine whether additional sanctions were appropriate.
Both players have the right to appeal the decision to the Court of Arbitration for Sport, the statement said.
South Korea's badminton association is scheduled to hold a news conference in Seoul later on Tuesday.
(Editing by Peter Rutherford)
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