Flights from Manila to Kota Kinabalu – Direct & connecting routes
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MNL to BKI – All flight route options from Ninoy Aquino International, Philippines to Kota Kinabalu International, Malaysia. These flights are operated by 3 airlines. Fly non-stop with Philippines AirAsia or choose from 1 different transit flights. The shortest flight time is 2 hours and 10 minutes. See the full flight schedule and time table, including departure times, airlines and stopover details to find the best option for you.
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Manila to Kota Kinabalu flights
There are over 2 and approximately 11 flights every week. You can fly non-stop to Kota Kinabalu (BKI) from Manila (MNL) with Philippines AirAsia or opt for a connecting flight via Bandar Seri Begawan (BWN).
Manila to Kota Kinabalu with Philippines AirAsia
You can fly non-stop every weekday with flights departing at 16:15, 20:35 or 23:10.
With Royal Brunei Airlines
If you fly from Manila with Royal Brunei Airlines you will do a stopover in Bandar Seri Begawan, BWN before reaching Kota Kinabalu. This flight trip will take 4 hours and 48 minutes and you can fly every Saturday with departures at 15:00.
Distance & flight times: Ninoy Aquino International to Kota Kinabalu International
The shortest flight time between MNL and BKI is 2 hours and 10 minutes.
Via | Total flight time | Layover time | Distance |
---|---|---|---|
Direct | 2h 10m | - | 685 miles (1102 km) |
BWN Bandar Seri Begawan | 4h 48m | 1h 10m | 889 miles (1430 km) |


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From Manila to Malaysia
Below is a list of other destinations to Malaysia from Ninoy Aquino International with either direct flights or 1 stop connections.
From Philippines to Kota Kinabalu
Below is a list of other cities in Philippines with flights to Kota Kinabalu with either non-stop or connecting flights.