This was the first outside investment in Facebook, and put the valuation of the company at US$4.9 million.
Facebook shares have surged 58 per cent this year.
Thiel has a reported net worth of US$3.2 billion, including a stake in data analytics company Palantir Technologies Inc.
Last month he got married in Vienna, Austria, to his longtime boyfriend.
The billionaire venture capitalist tied the knot with Matt Danzeisen, Axios reported.
The couple's wedding was reportedly a surprise to guests who thought they were celebrating Thiel's 50th birthday.
Danzeisen works as a portfolio manager at Thiel Capital, but not much is known about his position at the company.
Thiel has not commented publicly about the wedding or Danzeisen.
Back in May Danzeisen spoke about the state of financial technology at a conference in Japan.
"What might explain some of the slowdown is that winners are emerging as certain business models are becoming more clearly dominant," Danzeisen said at the time. "So, it is cyclical, but we'll still see innovation."
Thiel was a major supporter Donald Trump prior to the 2016 presidential election.
But Danzeisen was "much more moderate" in his support for Trump, Buzzfeed reported.
Since Trump took over the White House in January, Thiel has kept a quite and low profile.
He reportedly recently invested in a startup called 3T Biosciences with early Facebook investor Sean Parker.
The startup aims to build technology to fight cancer cells.
How Thiel backed Facebook
In his book The Facebook Effect, David Kirkpatrick outlines how Thiel came to make this investment: Napster co-founder Sean Parker, who at the time had assumed the title of 'President' of Facebook, was seeking investors for Facebook.
Parker approached Reid Hoffman, the CEO of work-based social network LinkedIn.
Hoffman liked Facebook but declined to be the lead investor because of the potential for conflict of interest with his duties as LinkedIn CEO. He directed Parker to Thiel, whom he knew from their PayPal days.
Thiel met Parker and Mark Zuckerberg, the Harvard student who had founded Facebook.
Thiel and Zuckerberg got along well and Thiel agreed to lead Facebook's seed round with US$500,000 for 10.2% of the company.