Five boys were on Sunday night busted in a Cardinal Otunga Girl's High School dormitory.
The five are said to have dressed in the school's uniform and disguised as girls.
Administrators called the police who arrested the five and frog-marched them to Bungoma police station.
The arrest of the boys turned the girls wild and sparked a protest that led to destruction in the school.
The five are said to be from the neighbouring St Mary's Kibabii Boys High School.
Police said they suspect the boys conspired with the girls during the day as a section of the girls had attended a sports event at St Mary's Kibabii.