In a post on Facebook, Koum did not give any reason for leaving WhatsApp which is by far the most widely used messaging platform globally, with 1.5 billion users.
But his exit comes in the wake of privacy scandals at Facebook, with the social media giant having admitted to leaks of most of its users' data. One political marketing company, Cambridge Analytica, that was part of Donald Trump's campaign, was given access to the data of 87 million users.
"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," Koum said in his Facebook post.
"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."
Koum and Acton started WhatsApp in 2009, charging US$0.99 annually for private communications and gathered almost 500 million users by 2014, according to the Washington Post. WhatsApp has never made any profits.
The WhatsApp founders added end-to-end encryption to the app in 2016. Their philosophy of collecting as little data as possible from their users appears to clash with Facebook's policy of snooping on users to the extent possible.
Acton, who left WhatsApp in November last year, has donated US$50 million to Signal, a messaging app made by Open Whisper Systems, and is now executive chairman of the non-profit Signal Foundation.
In a February blog post on the Signal Foundation site, Acton wrote: "(Signal founder) Moxie (Marlinspike) and I share a belief that the best way to continue to ensure the universal availability of high-security and low-cost communications services like Signal is to do so through a foundation structure that is free of the inherent limitations of a for-profit company.
"Moxie and his team have built something very special in Signal Messenger and I am thrilled to join their effort to provide the most trusted communications experience on the planet."