"Such a shelter will enable thousands of Kharkiv children to continue their safe face-to-face education even during missile threats," Mayor Ihor Terekhov wrote on the Telegram messaging app.
While many schools in the frontline regions have been forced to teach online throughout the war, Kharkiv has organised some 60 separate classrooms throughout its metro stations before the school year that started September 1, creating space for more than 1,000 children to study there.
Kharkiv, Ukraine's second largest city, had a population of more than 1.4 million before Russia invaded Ukraine in February 2022.
Parts of the city lie less than 35km from the Russian border and it has been subject to nearly daily Russian rocket and missile attacks that can hit before residents can reach shelters.
In the 24 hours to Monday, a civilian man died and several houses were damaged as a result of Russia's shelling and rocket attacks, Oleh Sinehubov, the governor of the Kharkiv region of which the city of Kharkiv is its administrative centre, said.
The war, which has no end in sight, has killed thousands and displaced millions of civilians. Ukraine's ministry of educations says that 363 educational institutions have been destroyed and nearly 3,800 damaged throughout the country.
The new school will "meet the most modern regulatory requirements for protective structures," Terekhov said.
It was not immediately clear how big the school will be or when it will open.