Gianni Infantino won with a majority in the second round of voting-gaining 115 votes from the representatives of 209 nations.
He pledged to rebuild the scandal-hit organization.
“I want to work with all of you together, with all of you,in order to restore and rebuild a new era in FIFA, a new era in FIFA where we can put again football in the center of the stage."
Infantino won 27 more votes than his closest rival-the favorite, Bahrain's Sheikh Salman al-Khalifa.
The Swiss-Italian lawyer was secretary-general at European football's governing body, UEFA.
His former boss at UEFA, Michel Platini, was implicated in a $2 million corruption scandal that also swept away the former president of FIFA, Sepp Blatter.
Both Platini and Blatter have been banned from football for six years.
That opened the route for Infantino's shot at the FIFA presidency.
Sports historian Philip Barker says Infantino has tried to reach out to smaller footballing nations.
“He has also offered to expand the World Cup to 40 teams.
A lot of countries are going to be greatly attracted by the increased prospects of qualifying for the greatest football show on Earth.”
Hours before the election, FIFA passed a set of reforms aimed at cleaning up its image.
It will have an elected council to replace the tarnished Executive Committee-with more female members to boost women's football.
The salaries of all senior figures will be disclosed.
And the presidency will be limited to a maximum of twelve years.
Many believe the reforms don't go far enough, says Barker.
“Twelve years, there's still ample time for corrupt practices.
Salary disclosure is another one that's a little bit difficult to pin down.
What expenses they take as well as the salary disclosure-that would be a real measure of just how transparent they're going to be."
U.S. and Swiss prosecutors are still investigating-and the full extent of criminal activity in FIFA is not yet known.
Gianni Infantino faces the task of restoring the image of a body that has become a byword for corruption.