The Dane polled 145 votes Saturday to beat Justian Suhandinata of Indonesia by 25 votes, becoming the first European to lead the Badminton World Federation since 1993.
Hoyer won the singles gold medal at the 1996 Atlanta Olympics. He succeeds Kang Young Joong of South Korean, who stepped down after eight years in charge.
Hoyer says eradicating "match-fixing or match-throwing" and ensuring badminton is in the top 10 of Olympic sports are among his top priorities.
The sport was disgraced at last year's London Olympics when eight Asian female players were disqualified for trying to lose matches to gain more favorable draws.