Learning was paralysed at Kolunga Primary School in Nyando after the night guard was found killed in one of the classrooms.
Pupils found the body of David Lusi, 40, lying in a pool of blood in the Standard Eight classroom, with a jembe, suspected to have been used in the murder lying nearby.
The guard escaped an attack last month. There were blood stains about 10 metres outside, indicating that his body might have been dragged into the classroom after being killed outside.
Teachers said Lusi's children were among the first pupils to stumble on the body as they reported to school.
The school's head teacher, David Owili, said the children were traumatised and some of them had run back home crying.
"We could not continue with learning under this situation and we have consulted stakeholders who advised that we send the children home," said Mr Owili.
Last month, the father of five was attacked by thieves who broke into the administration block and stole a projector, three laptops, a server, an unknown number of textbooks, and food.