In primary schools, only grade four and class eight pupils will resume face to face learning from Monday.
Form four students in secondary schools are also reporting back to schools to prepare for national examinations scheduled for March.
Ordinarily, the final year students would have sat for the examinations at the end of this year.
Kenya’s national teachers’ union Secretary General, Wilson Sossion, told the BBC Newsday programme that the reopening was being done cautiously.
“All schools must implement Covid-19 protocols in readiness for admission of students like one they must sanitise and provide sufficient hand-washing points, all learners must wear face masks, social distancing is encouraged though we have seen in some cases its impossible,” he said.
Mr Sossion said there was no guarantee that infections would not spike after schools reopen and said new cases will be dealt with if they occur, but that schools would not all close again.
Teachers in Kenya reported back to school two weeks ago to prepare for the resumption of face to face learning.
Kenya has so far confirmed 41,546 coronavirus cases.