The man, identified only by his surname Lee, allegedly posted the threat on the White House website earlier this month.
According to Yonhap, Lee, who denies guilt, was arrested on July 14 at the request of US authorities and found to have draft copies of the letter on his laptop.
Ambassador Mark Lippert was injured in an knife attack in Seoul in March.
He suffered deep gashes to his face and hand when Korean nationalist Kim Ki-jong lunged at him with a knife at a breakfast meeting in a hotel.
Kim Ki-jong is on trial for a string of charges linked to the attack.
Yonhap said that as well as the draft letter – the details of which have not been made public – Lee’s confiscated laptop showed he had visited the White House homepage and was storing a screen grab of when he posted the letter.
Police told Yonhap they believed Lee was acting alone.
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