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Cheap flights from Manila to Kota Kinabalu from $60

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 12/17. 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 (MNL-BKI)

Cheap round-trip flights

Philippines AirAsia Logo
11:10 pm - 1:20 amMNL-BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 amBKI-MNL
2h 10mnonstop
$98Philippines AirAsia
Find Deal
Sat, Sep 27 - Tue, Oct 7
Philippines AirAsia Logo
11:10 pm - 1:20 amMNL-BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 amBKI-MNL
2h 10mnonstop
$101Philippines AirAsia
Find Deal
Sat, Oct 4 - Fri, Oct 10
Philippines AirAsia Logo
11:10 pm - 1:20 amMNL-BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 amBKI-MNL
2h 10mnonstop
$106Philippines AirAsia
Find Deal
Wed, Oct 8 - Sun, Oct 12
Philippines AirAsia Logo
11:10 pm - 1:20 amMNL-BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 amBKI-MNL
2h 10mnonstop
$115Philippines AirAsia
Find Deal
Fri, Sep 19 - Thu, Sep 25
Logo
9:15 pm - 9:25 amMNL-BKI
12h 10m1 stop
Logo
1:45 am - 3:55 amBKI-MNL
2h 10mnonstop
$180
Find Deal
Sat, Oct 4 - Fri, Oct 10
Logo
11:10 pm - 1:20 amMNL-BKI
2h 10mnonstop
Logo
3:25 pm - 5:40 amBKI-MNL
14h 15m2 stops
$191
Find Deal
Sat, Oct 4 - Sat, Oct 11
Scoot Logo
7:35 pm - 11:15 amMNL-BKI
15h 40m1 stop
Scoot Logo
8:00 pm - 6:30 pmBKI-MNL
22h 30m1 stop
$214Scoot
Find Deal
Fri, Oct 24 - Fri, Oct 31
Scoot Logo
6:55 am - 7:25 pmMNL-BKI
12h 30m1 stop
Scoot Logo
8:25 pm - 5:40 amBKI-MNL
9h 15m1 stop
$232Scoot
Find Deal
Wed, Oct 8 - Mon, Oct 13
AirAsia Logo
10:45 pm - 8:40 amMNL-BKI
9h 55m1 stop
AirAsia Logo
11:45 am - 10:10 pmBKI-MNL
10h 25m1 stop
$303AirAsia
Find Deal
Wed, Sep 3 - Wed, Sep 10
Philippine Airlines Logo
7:20 am - 11:40 pmMNL-BKI
16h 20m1 stop
Philippine Airlines Logo
6:50 am - 4:20 pmBKI-MNL
9h 30m1 stop
$328Philippine Airlines
Find Deal
Wed, Oct 8 - Mon, Oct 13

Scoot flights from Manila to Kota Kinabalu

Our best Scoot deals on Manila to Kota Kinabalu flight tickets
Scoot
Oct 24
MNL7:35 pmManila Ninoy Aquino Intl
15h 40m
1 stop
BKI11:15 amKota Kinabalu
Oct 31
BKI8:00 pmKota Kinabalu
22h 30m
1 stop
MNL6:30 pmManila Ninoy Aquino Intl
$214
Find similar
Scoot
Oct 8
MNL6:55 amManila Ninoy Aquino Intl
12h 30m
1 stop
BKI7:25 pmKota Kinabalu
Oct 13
BKI8:25 pmKota Kinabalu
9h 15m
1 stop
MNL5:40 amManila Ninoy Aquino Intl
$232
Find similar

Philippines AirAsia flights from Manila to Kota Kinabalu

Our best Philippines AirAsia deals on Manila to Kota Kinabalu flight tickets
Philippines AirAsia
Sep 27
MNL11:10 pmManila Ninoy Aquino Intl
2h 10m
BKI1:20 amKota Kinabalu
Oct 7
BKI1:45 amKota Kinabalu
2h 10m
MNL3:55 amManila Ninoy Aquino Intl
$98
Find similar
Philippines AirAsia
Oct 4
MNL11:10 pmManila Ninoy Aquino Intl
2h 10m
BKI1:20 amKota Kinabalu
Oct 10
BKI1:45 amKota Kinabalu
2h 10m
MNL3:55 amManila Ninoy Aquino Intl
$101
Find similar
Philippines AirAsia
Oct 8
MNL11:10 pmManila Ninoy Aquino Intl
2h 10m
BKI1:20 amKota Kinabalu
Oct 12
BKI1:45 amKota Kinabalu
2h 10m
MNL3:55 amManila Ninoy Aquino Intl
$106
Find similar

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 August 20, 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

Sat 9/27

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Tue 10/7

1:45 am-3:55 am

Nonstop2h 10m

$98

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sat 10/4

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Fri 10/10

1:45 am-3:55 am

Nonstop2h 10m

$101

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 10/8

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Sun 10/12

1:45 am-3:55 am

Nonstop2h 10m

$106

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Fri 9/19

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Thu 9/25

1:45 am-3:55 am

Nonstop2h 10m

$115

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sat 10/4

9:15 pm-9:25 am

1 stop12h 10m

Kota Kinabalu

Fri 10/10

1:45 am-3:55 am

Nonstop2h 10m

$180

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sat 10/4

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Sat 10/11

3:25 pm-5:40 am

2 stops14h 15m

$191

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Fri 10/24

7:35 pm-11:15 am

1 stop15h 40m

Kota Kinabalu

Fri 10/31

8:00 pm-6:30 pm

1 stop22h 30m

$214

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 10/8

6:55 am-7:25 pm

1 stop12h 30m

Kota Kinabalu

Mon 10/13

8:25 pm-5:40 am

1 stop9h 15m

$232

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 9/3

10:45 pm-8:40 am

1 stop9h 55m

Kota Kinabalu

Wed 9/10

11:45 am-10:10 pm

1 stop10h 25m

$303

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 10/8

7:20 am-11:40 pm

1 stop16h 20m

Kota Kinabalu

Mon 10/13

6:50 am-4:20 pm

1 stop9h 30m

$328

Flights are sorted by cheapest round-trip flights first.

Showing 1-10 of 15 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 June is another great option to travel to Kota Kinabalu, with average flight prices from Manila averaging around $92.

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 are 1 cabin classes 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 August 2025, prices for Manila to Kota Kinabalu flights are approximately 15% 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

$41

Fastest flight time

2h 10m

Direct flights

Mon, Tue, Wed, Thu, Sat and Sun

Airports in Kota Kinabalu

1 airport
The best one-way flight to Kota Kinabalu from Manila in the past 72 hours is $41. The best round-trip flight deal from Manila to Kota Kinabalu found on momondo in the last 72 hours is $100.
The fastest flight from Manila to Kota Kinabalu takes 2h 10m
Direct flights go from Manila to Kota Kinabalu on Monday, Tuesday, Wednesday, Thursday, Saturday and Sunday. The only airline offering direct flights is Philippines AirAsia.
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
113 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 $106. 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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