Arora had been with WhatsApp since 2011 and through Facebook's $19 billion acquisition of the messaging company in 2014. His exit comes seven months after WhatsApp co-founder Jan Koum left the company.
"I am confident that WhatsApp will continue to be the simple, secure & trusted communication product for years to come," Arora wrote in a Facebook post Monday. He thanked Koum and WhatsApp co-founder Brian Acton, who left Facebook last year.
Arora's departure comes at a challenging time for WhatsApp, which has been dealing with the growing international problem of users spreading misinformation to large groups of people on the site. This year, WhatsApp deployed campaigns in top markets like India and Brazil to educate users and help them avoid sending around false information.
In addition to the recent departure of top WhatsApp executives, Facebook has also lost Instagram co-founders Kevin Systrom and Mike Krieger and Oculus co-founder Brendan Iribe in recent months. Alex Stamos, who was Facebook's chief security officer, left in August.
"WhatsApp is grateful for the dedication, focus, and outstanding work of our early leaders and team," a company spokesperson said in a statement to CNBC. "We remain deeply committed to providing a way for people to communicate privately now and in the future."