Nine other men were also taken into custody by police in the Swiss canton (state) of Bern. The men are accused of having sexual relations with a 15-year-old girl.
The age of consent in Switzerland is 16.
Authorities identified none of the men by name, in line with Swiss privacy laws, but police spokesman Juerg Mosimann said 12 were current of former Thun players.
The sexual relations appeared to have occurred on more than one occasion, police said in a statement, adding that the encounters appeared largely consensual.
Police, who searched homes on Tuesday, said they were still investigating the cases. The girl, who has since turned 16, is receiving counseling.
It is illegal under Swiss law to have sex with a minor if the age difference is greater than three years. Police did not release the ages of any of the men they arrested.
Telephone calls placed with FC Thun were not answered.
The team stunned Europe in 2005 by qualifying for the group stage of the Champions League, the continent's top club soccer competition. With an annual budget smaller than the individual salaries of many top players, Thun was the smallest side ever to ever advance to that stage.