The 47-year-old, the only European to win a badminton gold at the Olympics, will replace South Korea's Kang Young-joong who vacated the post after eight years at the helm.
"Hoyer Larsen polled 145 votes to Suhandinata's 120. There was one spoilt ballot," the BWF said in a statement.
Hoyer Larsen will have four years to revive the sport, which came under fire at last year's Games when four women's doubles pairs from South Korea, China and Indonesia deliberately played to lose their matches in order to get a more favourable draw.
- Sports & Recreation