The state news agency BNA quoted Muza al-Naar, representing the prosecutor general, as saying the two were involved in an attack by some 150 people on a police station, when petrol bombs were thrown. It did not say when the incident took place.
The two minors, both aged 14, would appear before a juvenile court on August 7, sources in the Shia opposition said.
A Bahraini court on July 5 ordered an 11-year-old Shia boy charged with a security offence to be monitored by a social worker for one year. The arrest of Ali Hassan, who was earlier placed in a juvenile detention centre, had provoked protests by the Shia opposition.
The tiny Gulf kingdom was rocked last year by a Shia-led protest movement against the ruling Sunni regime, calling for a constitutional monarchy.