Zuckerberg was in the nation's capital, where he testified before Congress about Facebook's new cryptocurrency Libra.
Facebook confirmed the meeting on Wednesday.
"As is normal for a CEO of a major U.S. company, Mark accepted an invitation to have dinner with the President and First Lady at the White House," a Facebook spokesperson said in an emailed statement.
It is not known what was discussed at the meeting. Thiel is a Facebook board member and a major donor to Trump's campaign.
The White House declined to comment.
Thiel is also the chairman of Palantir, a private data technology company that has become one of the largest recipients of government defense contracts.