The learners' temperatures were checked and they were required to use sanitiser before entering classrooms.
There was excitement in most schools as the pupils were reunited, the BBC's Ferdinand Omondi reports from Nairobi.
The authorities say efforts have been made to ensure that pupils and teachers will be safe.
But Kenya's National Union of Teachers' Secretary General Wilson Sossion told the BBC's Newsday programme that the return to school plan was "inadequate".
