"We will open our airspace at six (pm, 1300 GMT) today" for inbound and outbound flights at Islamabad, Peshawar, Karachi and Quetta airports, Civil Aviation Authority (CAA) spokesman Aamir Mehboob told AFP.
Other airports would be opened "gradually", he said. The CAA tweeted that passengers should check with their airlines for more details.
The decision to close airspace on Wednesday came after a rare aerial dogfight between nuclear-armed India and Pakistan in the skies over the disputed territory of Kashmir ignited fears of an all-out conflict, with world powers rushing to urge restraint.
Both sides claimed to have shot each other's warplanes down, and one Indian pilot was captured. Pakistan has vowed he will be returned to India on Friday in an overture towards New Delhi.
The airspace closure disrupted major routes between Europe and South Asia, with mounting frustration from passengers stranded at international airports.
Thai Airways cancelled nearly 30 flights, affecting 5,000 passengers. The decision affected services to London, Munich, Paris, Brussels, Milan, Vienna, Stockholm, Zurich, Copenhagen and Oslo.
Singapore Airlines was also forced to divert Europe-bound flights to Mumbai and Dubai to refuel, while a flight to Frankfurt was cancelled.
Emirates, Qatar Airways, Saudi Airlines, and Air Canada were all also among other carriers forced to cancel and divert flights.
Pakistan's civil aviation authorities said they had allowed some flights to depart on Thursday.
They were an Emirates service from Peshawar to Dubai, an Air Arabia flight from Peshawar to Ras Al Khaimah in the UAE and a Qatar Airways flight from Peshawar to Doha.