Prayuth Chan-ocha was formally appointed to run the nation at the army headquarters.
The 86-year-old monarch, King Bhumibol Adulyadej, did not attend the ceremony.
The military seized power in the South East Asian nation last week, saying it planned to return stability to Thailand after months of unrest.
The move followed six months of political deadlock as protesters tried to oust the government of PM Yingluck Shinawatra. At least 28 people were killed and several hundred injured over the course of the protests.
But the coup – which removed an elected government – has drawn widespread international criticism.
Small anti-coup protests took place in Bangkok over the weekend, despite a military ban on gatherings of more than five people.
Experts have also warned that the coup is unlikely to heal divisions in a nation in which politics have become highly polarized.
Prayuth Chan-ocha, dressed in white military uniform, received the royal endorsement on Monday morning.
“To restore peace and order in the country and for sake of unity, the king appointed General Prayuth Chan-ocha as head of the National Council of Peace and Order to run the country,” the royal command seen by AFP news agency said.
The monarchy is highly respected and royal endorsement is seen as key to legitimizing the takeover.
Speaking afterwards, Prayuth Chan-ocha said the most important thing was “to keep peace and order in the country”.
Elections would take place as soon as possible, he said, but gave no timeframe. He also said he would have no choice but to use force if protests continued.
The ruling junta is expected to set up a national legislative assembly that will draw up a temporary constitution with a new prime minister.
Since taking power, the military has summoned and detained dozens of key political figures, including Yingluck Shinawatra. Journalists and academics are also among those who have been called in.
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