Schools in Rafah and Sheikh Zuweid will reopen soon, Education Minister Mahmoud Abul-Nasr told CBC channel on Sunday.
The local governor announced the suspension of schools on 19 November, citing security reasons.
There are 230 schools in Rafah and Sheikh Zuweid, with 35-40 students per class, according to the minister.
Security forces have killed and arrested hundreds of militants in an ongoing anti-insurgency campaign over the last 16 months
Civilians have also been caught up in the violence.
Authorities began demolishing houses and clearing residents along the Egyptian border with Gaza in order to set up a buffer zone as part of the operation against militants, after an attack by the latter which killed 30 soldiers on 24 October.
After the attack, the army announced a three-month state of emergency in North Sinai and a curfew from 5pm to 7am.