According to the country's civil aviation authority, operations will resume at 5 PM UAE time on Friday.
On Thursday several UAE carriers were allowed to leave the country.
However the planes were flying without passengers with pilots only permitted to bring the aircraft safely home.
Air Arabia's flight G9825 was the first plane to leave Peshawar, bound for the emirate of Ras Al Khaimah.
Emirates flight EK637 also took off from the city, heading to Dubai.

Trump postpones military strikes on Iranian power plants
Pilot, co-pilot killed after passenger jet hits fire truck at LaGuardia airport
Kuwait launches probe into espionage, state security cases
Trump, Iran threaten to escalate conflict with attacks on energy and water facilities
Fuel reservoir in Russia's Primorsk port on fire after drone attack, governor says
Ambulances from Jewish community organisation torched, UK police say
Israeli airstrikes kill four in Gaza, Palestinian officials say
Iran says Hormuz open to all but ‘enemy-linked’ ships
