The 12 Bosnian nationals were charged with "becoming part of a terrorist group and illegally participating in conflicts in Syria in Iraq" during 2013 and 2014, a prosecutors' statement said.
Some of the accused were detained while others were being kept under house arrest.
"An investigation against all of them has been ongoing for the past six moths," spokesman Boris Grubesic told AFP.
If found guilty the suspects face up to 20 years in jail under a law adopted by the Balkans country last year.
The country's inter-ethnic war in the 1990s attracted hundreds of Islamists from across the Arab world to support Muslim forces.
Most of the foreign fighters have now left, but their strict interpretation of Islam has been adopted by some Bosnian Muslims, who 20 years later fight alongside jihadists in Syria and Iraq.
Some 150 Bosnians are believed to have joined jihadist groups fighting in Iraq and Syria, with 50 others believed to have already returned to Bosnia from Middle East battlefields, according to the intelligence services.
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