Prayuth Chan-ocha, 60, was nominated on August 21 in a legislature hand-picked by the junta and made up of mostly military and police figures.
The general was the head of the army when he led a dramatic coup in May.
It followed months of intense political deadlock between Yingluck Shinawatra’s government and opposition parties that resulted in protests and clashes.
Prayuth Chan-ocha was chosen after all 197 members of Thailand’s National Assembly cast their votes on Thursday morning.
The vote in Parliament was little more than a formality, lasting just 15 minutes, as Gen. Prayuth Chan-ocha was the only candidate.
The assembly’s choice is expected to be approved by King Bhumibol Adulyadej later.
Although his role is meant to be an interim one as Prayuth Chn-ocha plans to hold a general election in late 2015.
He now wields enormous power and also still heads the military junta.
Prayuth Chn-ocha is expected to pick his new cabinet soon.
He has promised a root and branch reform of politics to prevent a return to the turmoil of recent years, offering a possible restoration of democratic rule next year.
However, critics believe his real priority is to destroy the political party of former PM Thaksin Shinawatra, which has won every election for the past 14 years, and to secure a delicate royal succession.
Such goals would require a much longer democratic timetable.
Concerns have mounted that the military is seeking to strengthen its hold on the country.
Besides hand-picking the national assembly, the junta issued an interim constitution in July that gives the military sweeping powers.
It is appointing a national reform council that would help to come up with a permanent constitution that would take effect by July 2015.
Prayuth Chan-ocha 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.
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