Sein was chosen by a majority of Myanmar's electoral committee, an unnamed official told the AFP news agency.
He was up against two other candidates selected by the upper and lower houses of parliament and members of the military earlier this week.
All three candidates belong to the Union Solidarity and Development Party (USDP), which is backed by the junta that has ruled Myanmar since 1962.
The two not selected as president, Tin Aung Myint Oo and Sai Mouk Kham, will serve as Sein's vice presidents.
Sein became prime minister in October 2007, after the death of his predecessor Soe Win. Shortly afterwards he was promoted to general within Myanmar's army, a rank which he resigned in order to run in elections last year.
He is known in Myanmar as "Mr Clean", according to the Democratic Voice of Burma news site, having remained free from the corruption allegations that have dogged many of Myanmar's other high-ranking politicians.
Myanmar held its first general elections for 20 years in 2010 as part of its "roadmap to democracy". A quarter of the seats were kept aside for the military before the vote had started, while the National League democracy boycotted the election and others complained of cheating and intimidation.