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Cheap flights from Manila to Kota Kinabalu from $56

This is the cheapest one-way flight price found by a momondo user in the last 72 hours by searching for a flight from Manila to Kota Kinabalu departing on 11/10. Fares may change, and may not be available for all flights or travel dates. Click the price to refresh the search for this deal.
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Find the cheapest flights from Manila to Kota Kinabalu

Cheap round-trip flights

Enter your travel dates to find the best prices.
Philippines AirAsia Logo
4:15 pm - 6:30 pmMNL-BKI
2h 15mnonstop
Philippines AirAsia Logo
6:55 pm - 8:55 pmBKI-MNL
2h 00mnonstop
$108Philippines AirAsia
Find Deal
Wed, Nov 5 - Wed, Nov 12
Philippines AirAsia Logo
4:15 pm - 6:30 pmMNL-BKI
2h 15mnonstop
Philippines AirAsia Logo
6:55 pm - 8:55 pmBKI-MNL
2h 00mnonstop
$112Philippines AirAsia
Find Deal
Sun, Nov 9 - Sun, Nov 16
Philippines AirAsia Logo
4:15 pm - 6:30 pmMNL-BKI
2h 15mnonstop
Philippines AirAsia Logo
6:55 pm - 8:55 pmBKI-MNL
2h 00mnonstop
$115Philippines AirAsia
Find Deal
Wed, Dec 3 - Mon, Dec 8
Philippines AirAsia Logo
4:15 pm - 6:30 pmMNL-BKI
2h 15mnonstop
Philippines AirAsia Logo
6:55 pm - 8:55 pmBKI-MNL
2h 00mnonstop
$119Philippines AirAsia
Find Deal
Wed, Nov 26 - Sun, Nov 30
Multiple Airlines Logo
4:15 pm - 6:30 pmMNL-BKI
2h 15mnonstop
Multiple Airlines Logo
8:30 am - 2:05 pmBKI-MNL
5h 35m1 stop
$194Multiple Airlines
Find Deal
Sun, Nov 9 - Sun, Nov 16
Multiple Airlines Logo
1:10 am - 9:35 amMNL-BKI
8h 25m1 stop
Multiple Airlines Logo
6:55 pm - 8:55 pmBKI-MNL
2h 00mnonstop
$199Multiple Airlines
Find Deal
Sat, Nov 8 - Sun, Nov 16
HK Express Logo
2:05 am - 12:30 amMNL-BKI
22h 25m1 stop
HK Express Logo
1:30 am - 1:20 amBKI-MNL
23h 50m1 stop
$254HK Express
Find Deal
Wed, Nov 26 - Wed, Dec 3
HK Express Logo
8:35 pm - 12:30 amMNL-BKI
27h 55m1 stop
HK Express Logo
1:30 am - 1:20 amBKI-MNL
23h 50m1 stop
$269HK Express
Find Deal
Thu, Nov 27 - Wed, Dec 3
Scoot Logo
7:30 pm - 7:00 pmMNL-BKI
23h 30m1 stop
Scoot Logo
11:50 am - 5:30 amBKI-MNL
17h 40m1 stop
$271Scoot
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Tue, Nov 4 - Tue, Nov 11
AirAsia Logo
10:45 pm - 9:25 amMNL-BKI
10h 40m1 stop
AirAsia Logo
10:40 pm - 12:15 pmBKI-MNL
13h 35m1 stop
$290AirAsia
Find Deal
Fri, Oct 24 - Mon, Oct 27

Philippines AirAsia flights from Manila to Kota Kinabalu

Our best Philippines AirAsia deals on Manila to Kota Kinabalu flight tickets
Philippines AirAsia
Nov 5
MNL4:15 pmManila Ninoy Aquino Intl
2h 15m
BKI6:30 pmKota Kinabalu
Nov 12
BKI6:55 pmKota Kinabalu
2h 00m
MNL8:55 pmManila Ninoy Aquino Intl
$108
Find similar
Philippines AirAsia
Nov 9
MNL4:15 pmManila Ninoy Aquino Intl
2h 15m
BKI6:30 pmKota Kinabalu
Nov 16
BKI6:55 pmKota Kinabalu
2h 00m
MNL8:55 pmManila Ninoy Aquino Intl
$112
Find similar
Philippines AirAsia
Dec 3
MNL4:15 pmManila Ninoy Aquino Intl
2h 15m
BKI6:30 pmKota Kinabalu
Dec 8
BKI6:55 pmKota Kinabalu
2h 00m
MNL8:55 pmManila Ninoy Aquino Intl
$115
Find similar

HK Express flights from Manila to Kota Kinabalu

Our best HK Express deals on Manila to Kota Kinabalu flight tickets
HK Express
Nov 26
MNL2:05 amManila Ninoy Aquino Intl
22h 25m
1 stop
BKI12:30 amKota Kinabalu
Dec 3
BKI1:30 amKota Kinabalu
23h 50m
1 stop
MNL1:20 amManila Ninoy Aquino Intl
$254
Find similar
HK Express
Nov 27
MNL8:35 pmManila Ninoy Aquino Intl
27h 55m
1 stop
BKI12:30 amKota Kinabalu
Dec 3
BKI1:30 amKota Kinabalu
23h 50m
1 stop
MNL1:20 amManila Ninoy Aquino Intl
$269
Find similar
HK Express
Dec 3
MNL8:35 pmManila Ninoy Aquino Intl
27h 55m
1 stop
BKI12:30 amKota Kinabalu
Dec 7
BKI1:30 amKota Kinabalu
23h 50m
1 stop
MNL1:20 amManila Ninoy Aquino Intl
$404
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momondo 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, momondo users made 832,500 searches. Data last updated October 14, 2025.
Use the filters below to find and compare flights from Manila to Kota Kinabalu that are best for you.

Fly from

Fly to

Route

Depart

Return

Price

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 11/5

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Wed 11/12

6:55 pm-8:55 pm

Nonstop2h 00m

$108

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 11/9

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Sun 11/16

6:55 pm-8:55 pm

Nonstop2h 00m

$112

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 12/3

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Mon 12/8

6:55 pm-8:55 pm

Nonstop2h 00m

$115

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 11/26

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Sun 11/30

6:55 pm-8:55 pm

Nonstop2h 00m

$119

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 11/9

4:15 pm-6:30 pm

Nonstop2h 15m

Kota Kinabalu

Sun 11/16

8:30 am-2:05 pm

1 stop5h 35m

$194

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sat 11/8

1:10 am-9:35 am

1 stop8h 25m

Kota Kinabalu

Sun 11/16

6:55 pm-8:55 pm

Nonstop2h 00m

$199

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 11/26

2:05 am-12:30 am

1 stop22h 25m

Kota Kinabalu

Wed 12/3

1:30 am-1:20 am

1 stop23h 50m

$254

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Thu 11/27

8:35 pm-12:30 am

1 stop27h 55m

Kota Kinabalu

Wed 12/3

1:30 am-1:20 am

1 stop23h 50m

$269

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Tue 11/4

7:30 pm-7:00 pm

1 stop23h 30m

Kota Kinabalu

Tue 11/11

11:50 am-5:30 am

1 stop17h 40m

$271

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Fri 10/24

10:45 pm-9:25 am

1 stop10h 40m

Kota Kinabalu

Mon 10/27

10:40 pm-12:15 pm

1 stop13h 35m

$290

Flights are sorted by cheapest round-trip flights first.

Showing 1-10 of 20 resultsSorted by cheapest first
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See travel insights to Kota Kinabalu from

How to get the cheapest flight ticket from Manila to Kota Kinabalu

Look no further. We've gone through all the searches for this route on momondo so you have the important information and insights to find the cheapest flight ticket for your trip

What is the cheapest month to fly to Kota Kinabalu?

In general, July is the cheapest month to fly from Manila to Kota Kinabalu. Due to it being the ‘off-season’ during this time, you can expect flight prices to be around $86. The month of August is another great option to travel to Kota Kinabalu, with average flight prices from Manila averaging around $89.

What is the cheapest day to depart on your flight to Kota Kinabalu?

According to our data, Friday is the cheapest day to fly to Kota Kinabalu from Manila. The lowest ticket price found for a Friday departure recently was $101. Keep in mind that prices can always vary depending on your route and whether or not you are flying domestic or international. Flights from Manila to Kota Kinabalu on a Sunday will generally be more expensive and average around $153. Keep in mind that these prices on both days could fluctuate depending on the season and the demand.

What is the cheapest time of day to depart on your flight to Kota Kinabalu?

According to our data, the cheapest time of day to fly to Kota Kinabalu is in the evening. momondo users have found flights departing from Manila to Kota Kinabalu in the evening for as low as $102. Keep in mind that these prices may fluctuate based on what airline you choose and the time of year you plan to travel. Flights to Kota Kinabalu are more costly in the afternoon, with an average ticket price of $125. Departure times in the afternoon fall within the peak daily travel times, which is why tickets can be more expensive.

What is the cheapest Manila Ninoy Aquino Intl to Kota Kinabalu flight route?

Fly from Manila Ninoy Aquino Intl to Kota Kinabalu for the best Manila Ninoy Aquino Intl - Kota Kinabalu flight prices

How far in advance should I book a flight to Kota Kinabalu?

You are more likely to see cheaper flights to Kota Kinabalu from Manila when booking weeks ahead of your departure date. In general, you can expect to find flights to Kota Kinabalu for around $111 when searching weeks out. However, flight prices might be lower outside of this timeframe. For example, people recently found flights to Kota Kinabalu from Manila for as low as $93 on momondo.

What cabin class options are available on Manila Ninoy Aquino Intl to Kota Kinabalu flights?

There is only 1 cabin class available to choose from on Manila Ninoy Aquino Intl to Kota Kinabalu flights. Cabin price and availability will vary by airline so perform a search above to find the right deals for you.

How have Manila to Kota Kinabalu flight prices changed over time?

As of October 2025, prices for Manila to Kota Kinabalu flights are approximately 18% more expensive when compared to flights at the same time last year.

When to book flights from Manila to Kota Kinabalu

Are you open to changing your travel dates? Check out the ideal times to fly from Manila to Kota Kinabalu according to our flight data. Find out which month and days have the cheapest flights.
Estimated round-trip price

Cheap Manila to Kota Kinabalu (MNL to BKI) flight deals and tips

Find info about flight duration, direct flights, and airports for your flight from Manila to Kota Kinabalu

Best Price Found

$116

Fastest flight time

2h 10m

Direct flights

Mon, Tue, Thu and Sat

Airports in Kota Kinabalu

1 airport
The best flight deal from Manila to Kota Kinabalu found on momondo in the last 72 hours is $116
The fastest flight from Manila to Kota Kinabalu takes 2h 10m
Direct flights go from Manila to Kota Kinabalu on Monday, Tuesday, Thursday and Saturday. There are no airlines offering direct flights.
There is 1 airport near Kota Kinabalu: Kota Kinabalu (BKI)
Search flight deals

  • How far is Manila Ninoy Aquino Intl to Kota Kinabalu by plane?

    The straight-line distance from Manila Ninoy Aquino Intl to Kota Kinabalu is 682.5 mi. Typically, this will take 2h 10m by plane in normal conditions.

  • When did momondo last update prices for flights from Manila Ninoy Aquino Intl Airport to Kota Kinabalu Airport?

    Prices for flights from Manila Ninoy Aquino Intl Airport to Kota Kinabalu Airport are updated daily.

  • How many operators does momondo search for flights from Manila Ninoy Aquino Intl Airport to Kota Kinabalu Airport?

  • How old do you have to be to fly from Manila Ninoy Aquino Intl Airport to Kota Kinabalu Airport?

    The minimum age a child must be to fly alone is five but airlines that offer an unaccompanied minor (UNMR) service will have their own age restrictions, including rules around flight length, timings, and stopovers. We always recommend checking with the individual airline you are booking with to travel from Manila Ninoy Aquino Intl Airport to Kota Kinabalu Airport.

  • What documentation or ID do you need to fly to Kota Kinabalu Airport?

    The required travel and health documents for your Kota Kinabalu Airport trip may vary depending on your itinerary and personal circumstances. As a general rule, you should carry multiple documents, including a national ID card or driver's license and a passport valid for six months after your intended arrival at Kota Kinabalu Airport. We recommend that you seek guidance from your airline or a reliable third party such as IATA.

  • What is the most popular plane model from Manila to Kota Kinabalu?

  • What is the most popular airline from Manila to Kota Kinabalu?

Best airlines flying from Manila to Kota Kinabalu

Compare and see reviews for airlines that fly from Manila to Kota Kinabalu with momondo
Airline
Rating
Free Cancellation
Price
Philippines AirAsiaPriceFrom $82Free CancellationRating
6.6
114 reviews
Search Philippines AirAsia flights

  • Philippines AirAsia Flights From Manila to Kota Kinabalu

    Philippines AirAsia is one of the most popular airlines flying from Manila to Kota Kinabalu, operating 6 flights/week on average for this route. A good Philippines AirAsia flight deal for Manila to Kota Kinabalu starts from $82 round-trip, up to an average price of $107. Our users have rated Philippines AirAsia at 6.6/10.

Why use momondo?

Why should I use momondo to find a flight deal from Manila to Kota Kinabalu?

To find the flight that best suits your needs, momondo gathers a range of flights from a large pool of different airlines and agents; you can then use our insights and filters to find and book the right flight to Kota Kinabalu from Manila.

Can I find flights from Manila to Kota Kinabalu with flexible booking policies on momondo?

Yes. All flights to Kota Kinabalu from Manila on momondo can be compared and filtered by various policies on offer, including flexible booking.

How can momondo help me find flights from Manila to Kota Kinabalu?

Once you have performed a search in the form on the page, momondo provides useful filters and insights. We can show you the cheapest days and times to fly as well as help filter your options to help you make an informed choice when booking flights to Kota Kinabalu from Manila.

I’m not ready to book a flight from Manila to Kota Kinabalu right now. Can momondo alert me if prices change?

Price alerts on flights to Kota Kinabalu from Manila are quick and easy to set up on momondo. Simply perform a search and select the price alert feature. It is as simple as that.

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