WhatsApp CEO Jan Koum is one of the other founders, and he will not leave the company. Acton applied for Facebook in 2009 after leaving a job at Yahoo, but he was not accepted.
Acton leads the engineering section internally for WhatsApp, and a source close to the company says he is a big proponent that pushes WhatsApp toward encryption. His role will not be filled with other employees, according to a company spokesman.
Acton announced his departure to his colleagues at a large WhatsApp meeting at Facebook headquarters on Tuesday, and sent the news to his Facebook page that same afternoon.
"I am very fortunate at the age I have the flexibility to take new risks and focus on what I love," Acton, 45, wrote in a Facebook post.
"I've decided to start a non-profit business focusing on nonprofits, technology and communication, this is something I think about for a while, and now it's time to just focus and execute.I'll have more things to share in some months ahead. "
It's not entirely clear what Acton will focus on with his new venture, but he certainly has a lot of money to get started. Forbes estimates Acton's net worth of US $ 6.5 billion.
Brian Acton's departure comes at a time when WhatsApp, which has 1.3 billion users, is preparing to make some money.
The company employs a number of key business positions, and sources say that WhatsApp is building several company products that will help businesses send messages and interact with customers using this app. Currently WhatsApp does not generate any revenue.