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.
