Htin Kyaw is a close ally of Aung San Suu Kyi, whose National League for Democracy (NLD) party swept to victory in historic elections in November.
He said his appointment was "Aung San Suu Kyi's victory".
Ms Suu Kyi is barred from the post by the constitution, but has said she will lead the country anyway.
How Suu Kyi could be more powerful outside the presidency
Htin Kyaw won with 360 of the 652 votes cast in the two houses of parliament, with MPs erupting into applause when the result was announced.
"Victory! This is sister Aung San Suu Kyi's victory. Thank you," Htin Kyaw said after winning.
At the scene: Jonah Fisher, BBC News, Nay Pyi Taw
Image copyright AP Image caption As well as being a writer himself, Htin Kyaw is the son of a national poet and the son-in-law of a founder of the pro-democracy movement
The end result when it finally came was entirely as expected, with a landslide victory for Ms Suu Kyi's man, Htin Kyaw.
Given the miseries that this country has suffered this was another incredible momentous occasion.
But if she was enjoying it , or reflecting on the sacrifices that were made to get here, Ms Suu Kyi gave no indication. Just as she has done since the election in November, the former pro-democracy campaigner avoided the media and made no public comment.
No doubt acting on her instructions (probably a taste of what's to come) Htin Kyaw remained elusive.
The only time I saw Myanmar's next president was at the end of a cordoned-off corridor, waiting for the arrival of Ms Suu Kyi.