Trouble started on Saturday night when the boys were denied the chance to watch the ongoing Euro 2016 matches, irking the students who claim that the school has recently introduced rules they deemed too tough.
The students raided the principal's office, school canteen as well as a laboratory at a neighboring school where they left a trail of destruction.
Intervention by the area police came in after the damage had already been done.
School principal Andrew Otara, who was from the just concluded school heads meeting, said he is yet to understand the tough rules the students are talking about.
The act by the rowdy students has been condemned by area leaders including Kisii county boss James Ongwae who visited the school on Sunday morning.
Ongwae has called on the authorities to take stern action against the culpable individuals.
Area County Commissioner, Kula Hache condemned the disparaging riot saying investigations are underway.
Several students are currently being held at Gesonso police station.
The incident in Kisii comes amid a worrying trend of increased student protests being reported across the country.