A senior official at the Seoul Metropolitan Police Agency said the man, identified by his surname Lee, had included the threat in a post written on the White House website.
Police gave no details on the contents of the "incoherent" posting, which was written in English.
The man was arrested on July 14 following a tip off from the US Embassy in Seoul.
On his confiscated laptop, records of access to the White House homepage were found, as well as a draft of the posting and a screen capture, police said.
Lee, who police described as jobless, living in seclusion and spending most of his time surfing the Internet, denied authorship of the posting.
Another man, Kim Ki-Jong, 56, has been charged with attempted murder for his March assault on Ambassador Lippert at a breakfast function in Seoul that left the ambassador needing 80 stitches to a deep gash on his cheek.
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