Koum's departure comes at a crucial time at Facebook as the company reels from revelations of Russian election manipulation, fake news, data leaks and more. Koum has long been an advocate of privacy, writing in 2014 about his experience growing up in the USSR when he feared communications would be monitored by the KGB . In 2012 he posted a salvo about Google's data collection, writing, "Your data isn't even in the picture. We are simply not interested in any of it."

The Washington Post, which earlier reported details of Koum's departure, said Koum would leave both WhatsApp and Facebook's board. An SEC filing also showed that Koum will not stand for re-election on Facebook's board.

"And I'll still be cheering WhatsApp on – just from the outside," he wrote.

Jan Koum said in a Facebook post on Monday that it was time to "move on" and take time to do things outside of technology.

The co-founder of WhatsApp — the messaging app that Facebook bought for $19 billion in 2014, its largest-ever acquisition — is leaving the company.

Koum's Monday post announcing his departure did not mention privacy concerns, and did not specifically address his roles in Facebook outside WhatsApp. But according to the Post, Koum was "worn down by the differences in approach," particularly around data targeting, encryption, ad-based revenue and mobile payments.

Facebook CEO Mark Zuckerberg responded to the post on Monday, writing he was thankful for what Koum taught him about "about encryption and its ability to take power from centralized systems and put it back in people's hands."

"Those values will always be at the heart of WhatsApp," Zuckerberg wrote in a comment on Koum's Facebook post. But Zuckerberg has also pushed WhatsApp to "move faster" to grow its business base, despite scrutiny from the European Commission surrounding the company.

Koum is leaving Facebook less than two months after fellow WhatsApp co-founder Brian Acton told his followers to delete Facebook's app. Acton left Facebook to help launch the Signal Foundation, which supports secure messaging service Signal.

Koum's 2014 employment offer from Facebook included restricted stock units with a four-year quarterly vesting period, indicating those options should be free by the end of the year. Kuom sold almost $2.83 billion in shares in 2017, far more than most technology executives.

Koum told an audience in January that the team missed Acton, but said he still goes to work because it's like he "won the lottery."

Facebook did not offer additional comment to CNBC on Koum's departure.

Here's Koum's full post:

It's been almost a decade since Brian and I started WhatsApp, and it's been an amazing journey with some of the best people. But it is time for me to move on. I've been blessed to work with such an incredibly small team and see how a crazy amount of focus can produce an app used by so many people all over the world. I'm leaving at a time when people are using WhatsApp in more ways than I could have imagined. The team is stronger than ever and it'll continue to do amazing things. I'm taking some time off to do things I enjoy outside of technology, such as collecting rare air-cooled Porsches, working on my cars and playing ultimate frisbee. And I'll still be cheering WhatsApp on – just from the outside. Thanks to everyone who has made this journey possible.

Here's Zuckerberg's response:

Jan: I will miss working so closely with you. I'm grateful for everything you've done to help connect the world, and for everything you've taught me, including about encryption and its ability to take power from centralized systems and put it back in people's hands. Those values will always be at the heart of WhatsApp.

This is a developing story, please check back for updates.