Only a limited number of Messenger users will be able to try out the feature for now, but Facebook says it plans to make it more widely available later this summer.
Messenger's secret conversations rely on technology from Open Whisper Systems, which also makes the free end-to-end encrypted messaging and voice call app Signal.
Facebook used the same technology to build end-to-end encryption into WhatsApp, which it owns, in a process completed earlier this year.
The company is following in the footsteps of Apple, whose iMessage system has protected users' conversations with end-to-end encryption since 2011.
Matthew Green, a Johns Hopkins University computer science professor who consulted with Facebook on their plans to deploy end-to-end encryption in Messenger, says he's increasingly seeing a sort of sea change in how developers view the technology.
"It's becoming a minimal requirement for deploying an app like this," Green said.
But having a major player in the instant messaging world such as Facebook dive into this space also extends the privacy protection to an audience that otherwise might not use it, according to Green.
"There are people who aren't going to download some special app, so the fact it is being built into the things they already use is a really big deal," Green said.