Three pupils died while at least 53 were admitted after lightning struck classrooms Mkulima Primary School in Kuresoi North Sub-county on Thursday evening.
The Grade Four and Five learners were in their classes when the incident took place at around 3pm.
Head teacher Thomas Sisa said they had just rushed back into the classrooms to seek shelter from the heavy rains. They had been out for games.
Mkulima Location Chief John Macharia Muhia said he received information about the tragedy from a Nyumba Kumi elder.
"I mobilised residents to rescue the pupils. Doctors are observing 45 who are still recovering from the shock," Mr Muhia told the Nation.
He urged the government to install lightning arresters in schools to prevent similar cases.
Nakuru Governor Lee Kinyanjui, in his condolence message to the families, said the county dispatched three ambulances to transfer four critically injured pupils to Nakuru Level Five Hospital.
"The department of health has also dispatched a team of clinical officers and nurses to Kuresoi Health Centre, where 30 are admitted," he said.