David Marcus has been president of the mobile payments giant since 2012, after joining a year earlier as vice-president of mobile. He will now join the world's largest social network, taking his mobile expertise with him.
In a statement after the markets closed, eBay's chief executive and president John Donahoe, who oversees PayPal as its subsidiary, made the announcement.
"We wish him well. He leaves behind a strong leadership team, committed to not skipping a beat on executing our plans, scaling product innovation and driving global growth," he said in prepared remarks.
Citing PayPal's expected long-term success and strong leadership team, Marcus said it was the "right time to make a change" by leading a smaller team at Facebook.
Facebook said its own statement that messaging remains a "core part" of its service, citing its 12 billion messages that are sent every day on the social network.
"We're excited by the potential to continue developing great new messaging experiences that better serve the Facebook community and reach even more people, and David will be leading these efforts," Facebook said in a statement.
It's not immediately clear who Marcus will report to at Facebook, or who will take on the role as PayPal's president in the near future.
Facebook ($FB) was up by 0.3 percent in after-hours trading on the Nasdaq stock exchange, while eBay ($EBAY) was down 1.6 percent, at the time of writing.
eBay and Facebook are expected to report their fiscal second-quarter earnings on July 16 and July 21 respectively.