Athwal has spent nearly nine years at the company and was formerly the director of revenue at Yahoo Inc.
The company said it planned to launch a search for a replacement.
The company also said on Friday that it had set a $6 billion buyback program for its Class A shares, beginning in the first quarter of 2017.
Facebook’s shares were up 1.1 percent at $118.24 in after-hours trading. The company had a market value of about $337 billion at close.