In a statement, the airline said Vivienne Tan, the company's executive vice-president, has been appointed officer-in-charge and will take over from Bautista after his retirement.
Under Bautista's leadership, Philippine Airlines pursued an expansion programme, ordering Airbus wide-body jets to grow its profitable overseas route network. The carrier also improved its service, securing it a 4-Star rating from Skytrax.
In January, Japan's ANA Holdings Inc acquired 9.5% of Philippine Airlines for $95 million to support its Asia growth strategy.
Philippine Airlines operates 98 aircraft, mostly Airbus jets, with a route network of more than 30 domestic and 40 international destinations.
The announcement of Bautista's retirement comes as rival Cebu Air Inc signed a $6 billion plane deal to buy 10 of Airbus's new long-range A321XLR passenger aircraft as well as 16 wide-body A330neos and five single-aisle A320neos.
(Reporting by Neil Jerome Morales in MANILA and Alistair Smout in PARIS; Editing by Muralikumar Anantharaman and Louise Heavens)
By Alistair Smout and Neil Jerome Morales