At the time, Mr Koum wrote that the deal would not have happened if WhatsApp "had to compromise on the core principles that will always define our company, our vision and our product".
Mr Koum posted his plan to depart on his Facebook page, saying the decision was emotional.
But according to the Washington Post, Koum has been clashing with his parent company over data privacy issues including whether it should weaken WhatsApp's end-to-end encryption, which it rolled out in 2016.
The Post, citing people familiar with internal WhatsApp discussions, said Koum was worn down by the differences in approach to privacy and security between WhatsApp and Facebook.More news: Syria monitor: Missile attack kills 26, mostly Iranians
"It's been nearly a decade since Brian [Acton] and I started WhatsApp, and it's been an unbelievable journey with some of the best people". "I'm taking some time off to do things I enjoy outside of technology". Facebook bought Whatsapp in 2014 for $19 billion in cash and stock.
However, 18 months later, Facebook pushed WhatsApp to change its terms of service to give the social network access to the personal data of WhatsApp users.
Acton, who left Facebook in September 2017, was one of the most startling people to declare their breakup with the social network, posting to Twitter in March: "It is time". The app has about 1.5 billion users worldwide. Jan Koum is a Ukrainian-American internet inventor and computer programmer. Facebook declined to comment on whether Koum would retain his board seat.
In a comment on Koum's farewell post, Facebook CEO Mark Zuckerberg chimed in to thank Koum for his service - and, seemingly, to reassert the company's commitment to encryption on WhatApp.
"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 centralised systems and put it back in people's hands".