£72 Cheap Flights from Manila (MNL) to Kota Kinabalu (BKI)

View £72 flight on Sat, 1 Aug 2026Opens in a new window

Popular airlines from Ninoy Aquino Intl. Airport (MNL) to Kota Kinabalu Intl. Airport (BKI)

  • Be in the know

    Get alerts if flight prices drop or rise*

  • Book smarter

    Save up to 25% on select hotels after you book a flight*

  • Earn twice

    Earn your airline miles on top of our rewards
    Sign in

Cheap Flights from Manila (MNL) to Kota Kinabalu (BKI)

Prices were available within the past 7 days and start at £72 for one-way flights and £165 for round trip, for the period specified. Prices and availability are subject to change. Additional terms apply.

Scoot
Mon, 15 Feb - Tue, 23 Feb
MNL
Manila
BKI
Kota Kinabalu
£165 Return, found 21 hours ago
£165
Return
found 21 hours ago
Select Scoot flight, departing Mon, 15 Feb from Manila to Kota Kinabalu, returning Tue, 23 Feb, priced at £165 found 21 hours ago
Scoot
Mon, 15 Feb - Tue, 23 Feb
MNL
Manila
BKI
Kota Kinabalu
£170 Return, found 21 hours ago
£170
Return
found 21 hours ago
Select Scoot flight, departing Mon, 15 Feb from Manila to Kota Kinabalu, returning Tue, 23 Feb, priced at £170 found 21 hours ago
Scoot
Mon, 15 Feb - Tue, 23 Feb
MNL
Manila
BKI
Kota Kinabalu
£170 Return, found 21 hours ago
£170
Return
found 21 hours ago
Select Scoot flight, departing Mon, 15 Feb from Manila to Kota Kinabalu, returning Tue, 23 Feb, priced at £170 found 21 hours ago
Scoot
Mon, 15 Feb - Tue, 23 Feb
MNL
Manila
BKI
Kota Kinabalu
£176 Return, found 21 hours ago
£176
Return
found 21 hours ago
Select Scoot flight, departing Mon, 15 Feb from Manila to Kota Kinabalu, returning Tue, 23 Feb, priced at £176 found 21 hours ago
Scoot
Fri, 26 Jun - Sun, 28 Jun
MNL
Manila
BKI
Kota Kinabalu
£179 Return, found 2 days ago
£179
Return
found 2 days ago
Select Scoot flight, departing Fri, 26 Jun from Manila to Kota Kinabalu, returning Sun, 28 Jun, priced at £179 found 2 days ago
Scoot
Fri, 19 Jun - Mon, 22 Jun
MNL
Manila
BKI
Kota Kinabalu
£184 Return, found 2 days ago
£184
Return
found 2 days ago
Select Scoot flight, departing Fri, 19 Jun from Manila to Kota Kinabalu, returning Mon, 22 Jun, priced at £184 found 2 days ago
Royal Brunei Airlines
Sun, 7 Feb - Thu, 11 Feb
MNL
Manila
BKI
Kota Kinabalu
£228 Return, found 4 days ago
£228
Return
found 4 days ago
Select Royal Brunei Airlines flight, departing Sun, 7 Feb from Manila to Kota Kinabalu, returning Thu, 11 Feb, priced at £228 found 4 days ago
Singapore Airlines
Fri, 14 Aug - Mon, 24 Aug
MNL
Manila
BKI
Kota Kinabalu
£287 Return, found 6 days ago
£287
Return
found 6 days ago
Select Singapore Airlines flight, departing Fri, 14 Aug from Manila to Kota Kinabalu, returning Mon, 24 Aug, priced at £287 found 6 days ago
China Southern Airlines
Tue, 1 Sept - Thu, 10 Sept
MNL
Manila
BKI
Kota Kinabalu
£337 Return, found 21 hours ago
£337
Return
found 21 hours ago
Select China Southern Airlines flight, departing Tue, 1 Sept from Manila to Kota Kinabalu, returning Thu, 10 Sept, priced at £337 found 21 hours ago
Cathay Pacific
Fri, 3 Jul - Thu, 9 Jul
MNL
Manila
BKI
Kota Kinabalu
£348 Return, found 3 days ago
£348
Return
found 3 days ago
Select Cathay Pacific flight, departing Fri, 3 Jul from Manila to Kota Kinabalu, returning Thu, 9 Jul, priced at £348 found 3 days ago

Frequently asked questions

Which airlines fly direct from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
Enter MNL to BKI and your travel dates, then apply the 'Nonstop' filter to see only direct flights.
How do I find cheap flights from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
To find a cheap flight from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.), be flexible with your dates. Traveling outside of peak vacation months and booking a mid-week flight can help you save. Early morning and late night flights are often more affordable, too. Expedia allows you to compare flight times, airlines and routes all in one place to find low fares. You can also set up Price Tracking and receive alerts when fares go up or down.
What is the best airline to fly with from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
The best airline to fly with from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) will differ from traveller to traveller. If you like to fly early, Z2 offers early morning flights. If price is the most important factor, Z2 typically offers the lowest fares. PR offers the most daily flights from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.), which is brilliant if flexibility is what you value most. The best carrier for this journey could also be the one you have a loyalty membership with, as flying with that airline or another airline within the same alliance could help you collect points or enjoy lounge access.
What is the best time to fly from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
The best time to fly is usually mid-week (Tuesday or Wednesday) and during early morning hours as flights tend to be cheaper, less crowded, and generally more on-time. Avoid major holidays and peak vacation seasons for smoother travel. Combining off-peak days and hours often gives the best combination of cost, comfort, and convenience.
How many flights per day from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
There are approximately 34 connecting flights per day from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.). Some common connection points include Hong Kong Intl. (HKG), Kuala Lumpur Intl. (KUL), and Changi (SIN).
What is the earliest flight from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
The earliest flight from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) typically departs at approximately 12:05 AM local time, operated by Singapore Airlines and Malaysia Airlines. This is a seasonal service active in February. An early departure like this can help maximise your time at your destination. To compare early flights on Expedia, select the "Early Morning" and "Morning" filters in your search.
What day of the week has the most flights from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
You'll find the most flights from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) on a Sunday, with around 30 flights available. This gives you plenty of options for your travel plans. Major airlines on this route include Cathay Pacific, Malaysia Airlines, and Philippine Airlines. Flight schedules are fairly consistent throughout the week, with Sunday offering only slightly more options compared to other days.
What are the most popular departure times for flights from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
The most popular departure times for flights from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) are in the morning, from 6am to 9am. About 30% of passengers prefer this time. Many major carriers, including Malaysia Airlines, Philippine Airlines and Cathay Pacific, offer flights during this window. This timing works well because it allows you to start your journey early and arrive at your destination with plenty of time to settle in.
How long does it take to fly from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
A nonstop flight from MNL to BKI typically takes around 2 hours 20 minutes, covering approximately 682 miles. Connecting flights on this route usually add 9 hours 30 minutes to your travel time. Keep in mind that actual flight times can vary due to wind patterns, weather, and air traffic.
Can you fly business or first class from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
Select the "Business class" and "First class" filters when looking for MNL to BKI flights on Expedia. This is the easiest way to compare prices, routes and flight times for your trip.
How do I earn miles on a Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) flight with Expedia?
It's easy to earn miles on a Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) flight when you book with Expedia. Before you confirm your booking, simply select your frequent flyer program and enter your program number. As a member of One Key™, you can also earn OneKeyCash™* on top of your airline miles when you book with Expedia. *Excludes taxes and fees. OneKeyCash is not redeemable for cash and can only be used on Expedia and other participating brands.
What airports do you fly into for Kota Kinabalu from Ninoy Aquino Intl. (MNL)?
If you're planning to travel to Kota Kinabalu from Ninoy Aquino Intl. (MNL), you can fly directly into Kota Kinabalu Intl. (BKI) Some flights may connect through major hubs like Hong Kong Intl. (HKG), Suvarnabhumi Intl. (BKK), Changi (SIN) before reaching Kota Kinabalu. Compare routes and airports on Expedia to find the best flight options for your travel plans.
Is it cheaper to buy a plane ticket from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) at the last minute?
Typically, booking a last minute flight from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) will be more expensive than booking in advance. As the departure date approaches, there are usually fewer seats available which can drive up the cost. However, if there's some wiggle room with your travel dates and times, you could bag a cheap last-minute fare.
Is it cheaper to book a Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) flight and hotel package?
Securing a Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) flight and hotel package is usually cheaper than booking separately. With Expedia, you can enjoy the ease of organizing your travels all in one place. Select from our extensive range of stays and then add flights, activities and car rentals to your booking. Bundle everything together, and you could save hundreds of dollars.
Can I cancel or change the date of my flight from Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.)?
If you booked your Manila (MNL-Ninoy Aquino Intl.) to Kota Kinabalu (BKI-Kota Kinabalu Intl.) flight within the last 24 hours, you may be able to modify or cancel it without any fees. Depending on the airline and the type of ticket you have, additional charges may apply for changes beyond this timeframe. Airline policies and contact information can be found in your itinerary or confirmation email. Or, head to our Customer Service portal if you'd like more information.

Travel information

Origin airport
Ninoy Aquino Intl.
Destination airport
Kota Kinabalu Intl.
Airlines serving
Cathay Pacific, China Southern Airlines, Malaysia Airlines, Philippine Airlines, Scoot, Singapore Airlines
Return price
£164
Distance
1090 km
Average flight time
2 hours 10 mins

Book with confidence

Compare flights from Manila to Kota Kinabalu easily and book with confidence

For travelling on business or for pleasure, Expedia makes it easy to book your flights from Manila to Kota Kinabalu. Operating between them flights per day, 20 airlines cover the route. And fly direct, getting you to Kota Kinabalu Intl. in just hours. If you have a preferred carrier, use our advanced search tool to find the right flight from Ninoy Aquino Intl. to Kota Kinabalu Intl..  

To make things even better, in the advanced search, you can also choose to fly economy, premium economy, business or first class, select your maximum number of stops, and pick your preferred departure and arrival time. You can also opt for refundable and direct flights. 

Grab a great deal on your flight from Ninoy Aquino Intl. (MNL) to Kota Kinabalu Intl. (BKI)

The easiest way to view the best deals on flights from Manila to Kota Kinabalu today is to enter your travel dates and hit search. From here, you can sort your results by price to see the cheapest flights first. Right now, return flights from Ninoy Aquino Intl. to Kota Kinabalu Intl. start at just £165 and range up to £348.  

To find an even better deal, try  

  • being flexible on your dates – midweek flights can be cheaper
  • looking for other airports near Manila and Kota Kinabalu
  • booking your flight during February, the cheapest month on this route
  • varying your flight times – early morning and late at night are sometimes cheaper 

Why you should book your Manila to Kota Kinabalu flight with Expedia!

We cater for all flight types, cabin classes and airlines. So whether you’re booking flights from Ninoy Aquino Intl. to Kota Kinabalu Intl. for a budget break or a business trip with a bit of pleasure thrown in, we make it easy to secure the seat that’s right for you.  

Thanks to our supersized inventory that offers great choice all in one place, you know you’ll get a great deal with Expedia. Especially if you bundle your flight together with your hotel, you will unlock amazing savings. For added peace of mind, you can choose flexible bookings or filter to find refundable options, so you won’t pay a fee to change your flight.  

Compare flights from Manila to Kota Kinabalu easily and book with confidence

Explore a world of travel with Expedia

*Available to Expedia members.