Aleksander Ceferin has been elected the new UEFA president after receiving 42 of 55 votes.
The Slovenian will replace Michel Platini, who was forced to step down after being issued with a lengthy ban from all football activity.
Platini held office for eight years until he was alleged to have received a "disloyal" payment of £1.3m from former FIFA president Sepp Blatter.
Ceferin was up against Michael van Praag, who was backed by the English FA, but the Dutchman only received 13 votes from member nations.
The Slovenian, who has vowed to crack down on match-fixing, told Congress: "My dear friends, thank you for your fantastic support. It means a lot to me, my small and beautiful Slovenia is very proud of it, and I hope that one day you will also be proud of me."
Ceferin has been president of the Slovenian Football Association since 2011.
