The centre-back is the first player to ever make the move since both nations became independent following the break up of Yugoslavia.
Tensions still simmer away in the aftermath of the Bosnian War in the early to mid-90s, and the player does risk becoming very unpopular in his homeland.
Simunovic, though, having been ignored by the Croatian national team side despite representing his country at youth, is eager to start his international career.
Simunovic said: “I have decided to play for Bosnia and Herzegovina.
“My parents and my grandparents are all from Bosnia and Herzegovina. I was contacted by national coach Mehmed Bazdarevic and after our first meeting he gave me time to think about it.
“I then spoke to all my family and decided to play for my country.
“After that, I had several more meetings with Mehmed Bazdarevic and came to the definite decision I wanted to play for him and Bosnia and Herzegovina.”