Acton, who left WhatsApp in November previous 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.
Koum's departure follows in the footsteps of co-founder Brian Acton leaving the company last September. In March, The New York Times reported that Alex Stamos, Facebook's chief information security officer, meant to leave the company after an internal dispute over how to handle the threat of Russian influence efforts.
In a Monday Facebook post, Koum wrote it was time for him to "move on".
"But it is time for me to move on". In a post on Facebook, he said he was "taking some time off to do things I enjoy outside of technology". "And I'll still be cheering WhatsApp on - just from the outside".
Facebook chief executive Mark Zuckerberg testified before Congress earlier this month and apologized for inadequately protecting the data of millions of social media platform users.
Mr. Koum's exit is the highest-profile departure from Facebook after months of controversy at the social network.
Facebook CEO Mark Zuckerberg posted on Koum's timeline, 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". However, the Post suggested in its report that attempts by Facebook "to use its personal data and weaken its encryption" had caused tensions between the two companies, with the recent data scandal involving Facebook and Cambridge Analytica contributing to "a climate of broader frustration with Facebook among WhatsApp employees", sources with knowledge of the matter told the news outlet.
Privacy was WhatsApp's hallmark, and especially important to Mr. Koum, who grew up in Soviet-era Ukraine.
The company rapidly gained global popularity, with some 450 million users by the time the founders agreed to sell to Facebook in February 2014, following five days of talks that ended on Valentine's Day. So when Zuckerberg made the pair a multi-billion-dollar offer they couldn't refuse, Koum and Acton insisted on assurances that the core values behind WhatsApp would stay in place.
Messrs. Koum and Acton had clauses in their contracts with Facebook that allowed an acceleration of their contracts if Facebook added advertising to the app. Mr. Koum's contract with Facebook wasn't supposed to end until November, the person familiar with the matter said.