Deepfakes are computer-generated clips that are designed to look real.
The social media company said in a blog that these videos distort reality and present a "significant challenge" for the technology industry.
While deepfakes are still relatively uncommon on the internet, they are becoming more prevalent.
AI software creates deepfakes of people - often politicians or celebrities - by merging, replacing, or superimposing content on to a video in a way that makes it look real.
Facebook said it would remove videos if it realised they had been edited in ways that weren't obvious to an average person, or if they misled a viewer into thinking that a person in a video said words they did not actually say.
"There are people who engage in media manipulation in order to mislead," wrote Monika Bickert, vice president of global policy management at Facebook in the blog.
Facebook staff and independent fact-checkers will be used to judge a video's authenticity.
The new policy will not apply to parody or satire videos.