Officials of the Education Department said the schools will remain closed tomorrow as a precautionary measure to avoid any law and order problem.
They said a decision on re-opening of schools will be taken after assessing the situation.
The separatists, under the banner of joint resistance leadership (JRL), extended the strike in Kashmir by another day.
Syed Ali Geelani, Mirwaiz Umar Farooq and Mohammad Yasin Malik said the protest shut down will continue on Tuesday and Wednesday (4 April), a spokesman of the JRL said.
A march has been called to move towards Shopian, the spokesman of the separatist grouping said.
He said the leaders will also address a public rally in Shopian.
"People have been asked to peacefully protest Shopian killings at their local mosques after prayers tomorrow," he added.