Win Myint, a close aide of Aung San Suu Kyi, has been a speaker in the lower house since 2012 and was widely tipped for the top job.
But his role will be essentially ceremonial, with Ms Suu Kyi acting as de facto president.
Htin Kyaw resigned as president last week, amid growing health concerns.
Parliament then had seven days to choose a successor, and voted from a short-list of the three vice-presidents on Wednesday.
Earlier last week, Win Myint, 66, had been made a vice-president, a further sign he was likely to assume the presidency.
As a long-time member of Ms Suu Kyi's National League for Democracy, he is seen as a Suu Kyi loyalist.
The other two vice-presidents were Myint Swe, who served as acting president after Htin Kyaw stepped down, and Henry Van Thio.
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