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Cheap flights from Manila to Kota Kinabalu from ₱3,200

This is the cheapest one-way flight price found by a Cheapflights user in the last 72 hours by searching for a flight departing on 10/15. Fares are subject to change and may not be available on all flights or dates of travel.
MNL — BKI
Oct 16 — Oct 231
1 adult
1 adult, Economy

Cheapflights Tip: The best prices from Manila Ninoy Aquino Intl to Kota Kinabalu are usually found in July or August, booked 71 days in advance, depart on a Tuesday or Thursday and return on a Friday

Cheap flight deals from Manila to Kota Kinabalu

Discover tips and strategies to find the most affordable flight options for your journey from Manila (MNL) to Kota Kinabalu (BKI). Learn about various techniques such as flexible date searches, comparing prices across and setting up price alerts. Use these methods to find the cheapest flights available for your travel needs. Data last updated September 16, 2025.

Round-trip from

₱5,885

One-way from

₱3,200

Popular in

January

Cheapest in

July

Average price

₱6,457

Good round-trip deal

₱5,820 or less

Good one-way deal

₱2,758 or less
Philippines AirAsia
  • Philippines AirAsia
  • 10/19-10/21
  • Nonstop
  • 4h 20m total
  • Manila to Kota Kinabalu
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Philippines AirAsia
  • Philippines AirAsia
  • 10/15
  • Nonstop
  • 2h 10m total
  • Manila to Kota Kinabalu
Search Deals
Highest demand for flights based on searches. 16% potential increase in price (₱72,011 potential increase over avg. RT price).
Search Deals
Cheapest flight prices on average. 2% potential price decrease (₱8,727 potential savings vs. average RT price).
Search Deals
Average for round-trip flights in September 2025
Search Deals
Price to beat on a round-trip flight from Manila Ninoy Aquino Intl to Kota Kinabalu.
Search Deals
Price to beat on a one-way flight from Manila Ninoy Aquino Intl to Kota Kinabalu.
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Find flight deals from Manila to Kota Kinabalu

Cheapest flights from Manila to Kota Kinabalu
Explore the most affordable flight options available from Manila to Kota Kinabalu. Find the lowest fares from popular airlines and budget airlines, with prices last updated on September 16, 2025.

Sun 10/1911:10 pmMNL - BKI
Nonstop2h 10mPhilippines AirAsia
Tue 10/211:45 amBKI - MNL
Nonstop2h 10mPhilippines AirAsia
Deal found 9/13₱5,885
Sun 10/1211:10 pmMNL - BKI
Nonstop2h 10mPhilippines AirAsia
Sat 10/181:45 amBKI - MNL
Nonstop2h 10mPhilippines AirAsia
Deal found 9/14₱5,942
Mon 10/611:10 pmMNL - BKI
Nonstop2h 10mPhilippines AirAsia
Sat 10/111:45 amBKI - MNL
Nonstop2h 10mPhilippines AirAsia
Deal found 9/14₱6,057
Fri 10/1011:10 pmMNL - BKI
Nonstop2h 10mPhilippines AirAsia
Sat 10/111:45 amBKI - MNL
Nonstop2h 10mPhilippines AirAsia
Deal found 9/16₱6,114
Wed 11/124:15 pmMNL - BKI
Nonstop2h 15mPhilippines AirAsia
Sun 11/166:55 pmBKI - MNL
Nonstop2h 00mPhilippines AirAsia
Deal found 9/14₱6,171
Tue 10/1411:10 pmMNL - BKI
Nonstop2h 10mPhilippines AirAsia
Mon 10/201:45 amBKI - MNL
Nonstop2h 10mPhilippines AirAsia
Deal found 9/14₱6,514
Sun 11/164:15 pmMNL - BKI
Nonstop2h 15mPhilippines AirAsia
Wed 11/196:55 pmBKI - MNL
Nonstop2h 00mPhilippines AirAsia
Deal found 9/14₱6,914
Fri 11/74:15 pmMNL - BKI
Nonstop2h 15mPhilippines AirAsia
Mon 11/106:55 pmBKI - MNL
Nonstop2h 00mPhilippines AirAsia
Deal found 9/16₱7,257
Wed 10/294:15 pmMNL - BKI
Nonstop2h 15mPhilippines AirAsia
Wed 11/56:55 pmBKI - MNL
Nonstop2h 00mPhilippines AirAsia
Deal found 9/14₱8,857
Wed 9/1711:10 pmMNL - BKI
Nonstop2h 10mPhilippines AirAsia
Mon 9/221:45 amBKI - MNL
Nonstop2h 10mPhilippines AirAsia
Deal found 9/14₱9,028
Wed 11/126:30 amMNL - BKI
1 stop12h 30mMultiple Airlines
Sun 11/166:55 pmBKI - MNL
Nonstop2h 00mMultiple Airlines
Deal found 9/14₱9,085

Cheapflights Fare Finder

 
Customize your flight search to find flights from Manila to Kota Kinabalu that fit within your specific budget. Explore options based on user searches and filter the results based on your desired price range. Find flights that match your budget for a cost-effective journey. Over the last 7 days, Cheapflights users made 411,093 searches. Data last updated September 16, 2025.
Use the filters below to find and compare flights from Manila to Kota Kinabalu that are best for you.

Fly from

Manila

Fly to

Kota Kinabalu

Route

Depart

Return

Price

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 10/19

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Tue 10/21

1:45 am-3:55 am

Nonstop2h 10m

₱5,885

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 11/12

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Sun 11/16

6:55 pm-8:55 pm

Nonstop2h 00m

₱6,171

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 2/15

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Fri 2/27

6:55 pm-8:55 pm

Nonstop2h 00m

₱7,200

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Fri 11/7

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Mon 11/10

6:55 pm-8:55 pm

Nonstop2h 00m

₱7,257

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Mon 10/6

6:55 am-7:25 pm

1 stop12h 30m

Kota Kinabalu

Sat 10/11

1:45 am-3:55 am

Nonstop2h 10m

₱9,656

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Tue 10/14

7:35 pm-7:25 pm

1 stop23h 50m

Kota Kinabalu

Mon 10/20

1:45 am-3:55 am

Nonstop2h 10m

₱9,828

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Fri 11/7

7:30 pm-11:05 am

1 stop15h 35m

Kota Kinabalu

Mon 11/10

6:55 pm-8:55 pm

Nonstop2h 00m

₱10,171

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Mon 9/29

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Sat 10/4

1:45 am-3:55 am

Nonstop2h 10m

₱10,342

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 10/19

6:55 am-5:10 pm

1 stop10h 15m

Kota Kinabalu

Tue 10/21

1:45 am-3:55 am

Nonstop2h 10m

₱10,456

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 10/15

11:10 pm-1:20 am

Nonstop2h 10m

₱3,200

Flights are sorted by cheapest round-trip flights first.

Deals found on 9/15

Showing 1-10 of 21 results
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Best time to book a flight from Manila to Kota Kinabalu

Have a flexible travel schedule? Discover the best time to fly to Kota Kinabalu from Manila with our price prediction graph.
Estimated round-trip price
Rates are based on past data. Find the cheapest month and day to book your flight based on your travel requirements, then search for cheap deals.

Cheapflights Insights

Everything you need to know about your flight from Manila to Kota Kinabalu

How far ahead should I book a flight from Manila to Kota Kinabalu?

Use this chart to determine the optimal time to book a round-trip flight from Manila to Kota Kinabalu. Price data was last updated on September 12, 2025.

The price you pay for your flight from Manila to Kota Kinabalu may vary depending on when you book. For the best chance of a lower fare, look to book 71 days in advance of your trip. Fares are likely to increase a fortnight or so before your departure date.

What is the cheapest month to book a flight from Manila to Kota Kinabalu?

Currently, January is the cheapest month in which you can book a flight from Manila to Kota Kinabalu (average of ₱83). Flying from Manila to Kota Kinabalu in December is currently the most expensive (average of ₱112). There are several factors that can impact the price of a flight, so comparing airlines, departure airports and flight times can provide users with more options.

What is the cheapest time of day to fly from MNL to BKI?

Find hourly flight availability from Manila to Kota Kinabalu. Discover flight options and departure times throughout the day, allowing you to choose a departure time that suits your schedule. Data last updated September 16, 2025.

It’s typically best to fly out from Manila to Kota Kinabalu in the evening. Doing so could potentially save you 53% on the flight price compared to flying at noon, which is usually more expensive.

Reviews of airlines servicing Kota Kinabalu

Get insights into the airlines that provide service to Kota Kinabalu. Read reviews, discover amenities, and learn about the overall travel experience offered by airlines. Use this information to make informed decisions when choosing an airline for your flight to Kota Kinabalu. Reviews last updated September 16, 2025.
Read reviews from past customers who have flown Malaysia Airlines, Scoot, and Philippines AirAsia from Manila to Kota Kinabalu. Users can see the overall rating for each airline as well as how each is rated in terms of entertainment options, comfort, food, crew/service, and boarding process.
Malaysia Airlines
7.3
Good
278 reviews
Check prices

Entertainment

6.7

Boarding

7.6

Comfort

7.4

Crew

8.1

Overall

7.3

Food

7.0

Reviews

1 / 20
8.0
Excellent

Anjan,Nov 2024

SYD - KUL

I have a good experience and got good hospitality from cabin crew thank you.
Malaysia Airlines
7.3
Good
278 reviews
Malaysia Airlines
7.3
Good
278 reviews
Check prices

Entertainment

6.7

Boarding

7.6

Comfort

7.4

Crew

8.1

Overall

7.3

Food

7.0

Reviews

1 / 20
8.0
Excellent

Anjan,Nov 2024

SYD - KUL

I have a good experience and got good hospitality from cabin crew thank you.
Scoot
6.7
Okay
308 reviews
Malaysia Airlines
7.3
Good
278 reviews
Check prices

Entertainment

6.7

Boarding

7.6

Comfort

7.4

Crew

8.1

Overall

7.3

Food

7.0

Reviews

1 / 20
8.0
Excellent

Anjan,Nov 2024

SYD - KUL

I have a good experience and got good hospitality from cabin crew thank you.
Philippines AirAsia
6.6
Okay
113 reviews
Malaysia Airlines
7.3
Good
278 reviews
Check prices

Entertainment

6.7

Boarding

7.6

Comfort

7.4

Crew

8.1

Overall

7.3

Food

7.0

Reviews

1 / 20
8.0
Excellent

Anjan,Nov 2024

SYD - KUL

I have a good experience and got good hospitality from cabin crew thank you.

Related info for your journey

Find useful and relevant information for your journey from Manila to Kota Kinabalu. Access travel guides, tips, and recommendations to enhance your travel experience. Get information about local attractions, weather, transportation options, and more.

  • How popular is this Manila to Kota Kinabalu flight route?

    This flight path from Manila Ninoy Aquino Intl to Kota Kinabalu was viewed by 1,342 users in the past month. Keep an eye out for changes in search interest prior to high and low season.

  • How long is the flight from Manila to Kota Kinabalu?

    There are many flights that can get you from Manila to Kota Kinabalu in 2h 10m. Fly via Philippines AirAsia to get the fastest option. The distance between Manila and Kota Kinabalu is about 1096 km. Generally, flights for this route are direct.

  • What are the cheapest airlines flying from Manila to Kota Kinabalu round-trip?

    Flying on Philippines AirAsia is currently your cheapest option to Kota Kinabalu, with prices starting at ₱4,290. Additional round-trip tickets that might be worth considering are offered by Scoot and Malaysia Airlines, with the lowest prices starting at ₱9,420 and ₱17,902, respectively. You may be able to fly from Manila to Kota Kinabalu for 31% less than the average price by searching for these airlines.

  • What are the cheapest flights from Manila to Kota Kinabalu?

    On average you can expect to pay ₱5,428 for a flight from Manila to Kota Kinabalu. The cheapest flight overall is ₱2,237 while the most popular route, (Manila Ninoy Aquino Intl - Kota Kinabalu) is currently priced at ₱6,171.

  • Can I find deals for flights from Manila to Kota Kinabalu that include hotel bookings?

    Yes. In addition to deals on Manila to Kota Kinabalu flights, Cheapflights offers vacation packages that include both flights and hotel.

  • How can I find direct flights from Manila to Kota Kinabalu?

    After entering your origin and destination, apply the non-stop filter on the search result page to find direct flights from Manila to Kota Kinabalu.

  • Can I find deals for business class flights from Manila to Kota Kinabalu?

    Yes. Cheapflights offers flight deals from Manila to Kota Kinabalu by cabin class. In addition to browsing deals, you can also filter by cabin class on the search results page after making a search.

  • What is the cheapest month to book a flight from Manila to Kota Kinabalu?

    Currently, January is the cheapest month in which you can book a flight from Manila to Kota Kinabalu (average of ₱83). Flying from Manila to Kota Kinabalu in December is currently the most expensive (average of ₱112). There are several factors that can impact the price of a flight, so comparing airlines, departure airports and flight times can provide users with more options.

See more FAQs

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Fly from Manila to Kota Kinabalu on these airlines

Choose from the following airlines for your flight from Manila to Kota Kinabalu. Flights are based on user searches made on Cheapflights and were last updated on September 16, 2025.
Philippines AirAsia flights from Manila Ninoy Aquino Intl to Kota Kinabalu
Scoot flights from Manila Ninoy Aquino Intl to Kota Kinabalu

Top 3 airlines flying from Manila to Kota Kinabalu

Discover the top 3 airlines that operate flights from Manila to Kota Kinabalu. Compare their services, reliability, and customer satisfaction ratings to choose the airline that best suits your travel preferences and needs. Over the last 7 days, Cheapflights users made 411,093 searches. Data last updated September 16, 2025.
AirlineCheapestAverageFlexibilityOn-time
Philippines AirAsiaCheapest₱4,290Average₱6,193FlexibilityNo cancel feeOn-time53%
Search Philippines AirAsia flights
ScootCheapest₱9,420Average₱10,534FlexibilityNo cancel feeOn-timeN/A
Search Scoot flights
Malaysia AirlinesCheapest₱17,902Average₱25,500FlexibilityNo cancel feeOn-time67%
Search Malaysia Airlines flights

Fly with Cheapflights

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How does Cheapflights help users find flights from Manila to Kota Kinabalu?

Cheapflights makes it easy to find Manila to Kota Kinabalu flights by helping our users search from 900+ travel sites for deals. We also provide you with filters for cabin, price, airline, airports, number of stops, and many more to narrow down that perfect flight.

Why should you use Cheapflights to find cheap flight tickets from Manila to Kota Kinabalu?

By finding flights from multiple airlines and providers at completely no cost, Cheapflights helps millions of users like you annually find the best flights to Kota Kinabalu from Manila.

Can Cheapflights find flights from Manila to Kota Kinabalu with no change fees?

Need flexible booking options for your flight to Kota Kinabalu from Manila? Don’t worry, Cheapflights have you covered. Use our search filter to only show flights with no change fees.

Can Cheapflights notify me if prices for flights from Manila to Kota Kinabalu become cheaper?

Yes, Cheapflights offers price alerts on Manila to Kota Kinabalu flights so you can book your travel at the perfect time. Price Alerts can be enabled by clicking the bell icon next to the flight deals above and providing your email address where you want to receive the alerts.

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