The Manchester City striker has lifted the award for a third consecutive time, despite only playing a handful of times for his country in five years
Bosnian website SportSport selected the 26-year-old ahead of Roma midfielder Miralem Pjanic, Lazio's Senad Lulic, Hoffenheim midfielder Sejad Salihovic and Stuttgart forward Vedad Ibisevic.
Stoke City goalkeeper Asmir Begovic won the award for the best Bosnian goalkeeper for last season.
"This is great honour for me, to win this award for third time in a row, with the competition like this," Dzeko told SportSport.
"I'm very satisfied with the season that is now behind us, even though I haven't played that much in second part of the season. At the end we won the title and that is the most important thing.
"I hope that we can defend the title this season too, but it will be very interesting. I guess Manchester United will be the strongest competition once again, and I would say that Chelsea will be boosted with Champions league trophy."