Azam Saigol tendered his resignation yesterday citing personal reasons without giving details, PIA spokesman Danyal Gilani confirmed.
The development comes as Pakistan International Airlines (PIA) is under fire over allegedly poor flight safety protocols, following the crash of its PK-661 flight.
The flight had smashed into a hillside in the country's north while travelling from the city of Chitral to Islamabad last Wednesday, killing all 47 people on board.
Saigol was appointed after previous chairman Nasser Jaffer resigned amid a controversy resulting from the countrywide strike by the airlines' employees over the government's reported privatisation plans.
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The protests incurred an estimated loss amounting to Rs 1.8 billion to the airline in a week.
PIA suffers billion of rupees of losses annually and the government has to inject 12 to 15 billion rupees every year to keep it in the air.
Saigol, who had remained on PIA's board of directors since 2013, is an Oxford educated and a well known industrialist.
PIA grounded all 10 French-built ATR turboprop planes in its fleet yesterday, saying it would now undergo thorough testing after the two bad incidents.
The national carrier has so far declined to comment while Pakistani authorities investigate the causes of the crash.
The plane had descended in an unsymmetrical manner after which it lost altitude in the few moments before it crashed in Saddha Batolni village near Havelian, killing all 47 people on board, including pop singer-turned-Islamic preacher Junaid Jamshed, his wife and Deputy Commissioner Chitral Osama Warraich.