Police said that 33-year-old Johan Cosar, a native of the ancient Syriac Christian community, was arrested in the city of Basel but was released after questioning over his decision to join anti-IS fighters.
He faces prosecution by Swiss military justice for joining a foreign army without official authorisation and risks up to three years behind bars if convicted.
Cosar's case comes as Western nations beef up efforts to stop pro-IS volunteers from leaving for Syria and Iraq and pledge to prosecute them on return.
The Swiss stance however contrasts with a Dutch response in October to reports that members of the No Surrender biker gang were fighting alongside Kurdish forces battling against IS in northern Iraq.
"Joining a foreign armed force was previously punishable, now it's no longer forbidden," public prosecutor spokesman Wim de Bruin told AFP at the time.
Britain too has seen citizens leave to fight by the side of Kurdish groups combatting IS, but there has been no official action against them as yet.
Cosar, who was born in Switzerland and received military training there, fought for more than two years in a Syriac militia defending members of the community in north-east Syria where they are under attack by IS fighters.
He said in an October interview with Swiss paper Tages Anzeiger that he first went to Syria as an independent journalist.
But shortly after arriving he met Syriac militia fighters and founded the Syriac Military Council to defend "a place, a religion, a history… humanity and democracy."
Syriacs, members of a Middle Eastern Orthodox Christian community, speak a form of Aramaic dating to the 12th century BC.
Christians have been forced to flee their homes by the tens of thousands in Iraq and Syria after attacks from IS fighters.
The UN Security Council is to meet on March 27 to oppose the growing persecution of Christians in the Middle East.
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