Khasoko Boys High School in Bumula has been shuttered indefinitely, with only the Form Four students staying to study.
It comes just a week after one of the school's students died while receiving treatment at the Bungoma County Referral Hospital.
The school principal, Daniel Masombo, told Citizen Digital over the phone that the post-mortem report revealed that the youngster died from severe malaria.
He said that the Ministry of Education recommended the school closure in the aftermath of student deaths in other schools in neighbouring Kakamega County.
According to Bungoma Health CEC Dr Andrew Wamalwa, the post-mortem examination also revealed that the student had developed a perforation in the stomach, which caused Peritonitis.
Peritonitis is a condition in which the thin layer of tissues inside the abdomen becomes inflamed due to a bacterial or fungal infection.
Dr Wamalwa stated that the county has already dispatched a team to the school to collect food and water samples, which will be transferred to Nairobi for additional investigation to determine the source of the virus.