The social media giant had been given until 10:00 local time (04:00 GMT) to remove 131 pages that Thailand said violated its strict lese-majeste laws.
More than 100 people have been charged under the law since the military coup three years ago.
Authorities had threatened legal action and a complete shutdown of Facebook.
Thais are among the biggest users of Facebook in Asia, with thousands of small businesses here relying on it as their main marketing tool.
If the government carries out its threat to prosecute Facebook, and even to force local internet service providers to block it, there will be a public outcry.
However, the government seems determined to ensure that no material it deems damaging to the monarchy is visible in Thailand, despite the challenge of doing this in an open economy, and in the digital information age.
It is especially sensitive about photographs of the new King Maha Vajiralongkorn which have been circulated by some critics of the monarchy.
The king, who succeeded his father last December, has had a colourful personal life, although the severe lese-majeste law makes any discussion of the monarchy impossible inside Thailand.
In 2015, when Facebook set up an office in Thailand, it said 34 million Thais were using Facebook every month, and that they posted three times more than the global average.
Most social media monitoring companies predict the number of users in Thailand has grown significantly since then.
The firm has previously said it carefully scrutinises requests made by governments wanting to restrict content.
If it determines the content does violate local laws it makes it unavailable in the country and notifies people who try to access it.