On 21 August he was named prime minister by the legislature, in a move that was widely expected.
Under Gen Prayuth, the military had hand-picked the legislature, populating it with mostly military and police figures. It also issued an interim constitution in July that gives the military sweeping powers.
Such moves have triggered concerns that the military is seeking to strengthen its hold on the country as it initiates political reform. But Gen Prayuth and junta officials have argued that military rule has brought stability to Thailand following months of violent protests between the pro- and anti-Thaksin camps.
Gen Prayuth began his military career in the prestigious Queen's Guard unit, which has nurtured other top army bosses, according to The Bangkok Post. The 21st of August happens to be Queen's Guard Day and is said to be an auspicious day for the general.
He climbed the ranks to become a commander in the King's Guard, before taking over as head of the army in October 2010.
He is seen as a staunch royalist, having favoured a tough stance against the "Red Shirt" protest movement supporting populist former Prime Minister Thaksin Shinawatra and the government of his sister Yingluck.
After taking over the army, Gen Prayuth said that he wanted the army to remain neutral, but some of his actions prompted questions over whether he was intervening in politics.
The pressure group Human Rights Watch said he had been "interfering" into an investigation into deadly political protests in 2010.
In May 2011, a prominent opposition MP and Red Shirt leader, Jatuporn Promphan, was imprisoned after being charged with making comments deemed to be disrespectful of the monarchy - a very serious offence in Thailand.
The case against him was prompted by a complaint from Gen Prayuth. He insisted at the time that his motive was not political but rather to protect the monarchy.
However, questions were again raised when in June 2011 he appealed for voters to back "good people" in that year's elections, in what was widely interpreted as a swipe at Ms Yingluck and her Pheu Thai party.
It nevertheless swept to power, winning a majority in parliament.
Pheu Thai had worked hard to cultivate good relations with Gen Prayuth and the other top echelons of the Thai military, and when there were mass protests last autumn over a controversial amnesty law Pheu Thai had proposed, he stayed silent on the issue.
However, as the protests dragged on, he proposed a "people's council" of civilians from both sides of the political divide.
Months of political conflict appeared to have forced Gen Prayuth's hand. He said he initiated the coup as a reaction to "the violence in Bangkok and many parts of the country that resulted in loss of innocent lives and property, [which] was likely to escalate".