The serious shortage of food and water means that more than 17,000 children would have to go home.
Across the Horn of Africa, a lack of rain has made drinking water scarce, harvests have failed, cattle has died, families have lost income and supplies, and food prices have soared.
Millions of children in Kenya, Somalia, and Ethiopia could die from malnutrition.
Unless the government helps, schools in northern Kenya would be forced to close early, said Ibrahim Maalim Hassan from Kenya’s Secondary School Heads Association.
“We are in a Catch-22 situation where we want the schools to go on, but the conditions on the ground are not conducive,” he said, adding that delays in distributing free secondary education funding is making things worse.
Rising food and fuel prices are making managing 65 public schools in the region a nightmare he said. “Last term, five schools were forced to close early because of water shortage, but it could be worse this term,” he told the country’s Daily Nation newspaper.
Mohamed Ibrahim Adam, the head of Arabia Girls’ Secondary School said: “Food and fuel prices in Mandera East have shot through the roof.” Basic foods such as beans and sugar what shot up to nearly five times their original price, since the drought started.
The Nakuru Boys’ High School principal also called on the government to address the famine situation in Turkana and Baringo.
Kenya’s government has declared the drought and food crisis a national disaster. Last month, people in the country took the government to court in a landmark case, claiming that their constitutional right to be free from hunger had been violated.
Every Kenyan's right to "be free from hunger and to have adequate food of acceptable quality" is protected in Article 43 of a new constitution, approved in a referendum last August.
Most Kenyans live below the poverty level of about 60p a day.
Millions of women walk further than six kilometers a day to find, water and firewood. This leaves little time for school, getting any medical treatment they or their families need and earning a living. Because of the drought in Kenya, many women are forced to walk even further, sometimes for several hours. Even once they arrive at a water point, there is often an equally long wait in a queue for water.