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 6/5. 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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Cheap round-trip flights

Enter your travel dates to find the best prices.
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$99Philippines AirAsia
Sun, Apr 12 - Sun, May 10
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$104Philippines AirAsia
Mon, Aug 10 - Wed, Aug 12
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$105Philippines AirAsia
Mon, Aug 10 - Wed, Aug 12
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$107Philippines AirAsia
Wed, Jun 17 - Fri, Jun 19
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$117Philippines AirAsia
Mon, May 4 - Fri, May 8
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$123Philippines AirAsia
Sun, Aug 23 - Fri, Aug 28
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$129Philippines AirAsia
Fri, Apr 17 - Sun, Apr 19
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$154Philippines AirAsia
Wed, May 27 - Fri, May 29
Philippines AirAsia Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Philippines AirAsia Logo
1:45 am - 3:55 am
BKI
-
MNL
2h 10mnonstop
$166Philippines AirAsia
Fri, Apr 3 - Sun, Apr 5
Multiple Airlines Logo
11:10 pm - 1:20 am
MNL
-
BKI
2h 10mnonstop
Multiple Airlines Logo
8:30 pm - 5:50 am
BKI
-
MNL
9h 20m
1 stop
$188Multiple Airlines
Sun, Apr 12 - Mon, May 11

Royal Brunei Airlines flights from Manila to Kota Kinabalu

Our best Royal Brunei Airlines deals on Manila to Kota Kinabalu flight tickets
Royal Brunei Airlines
Apr 9
MNL9:45 pmManila Ninoy Aquino Intl
23h 10m
1 stop
BKI8:55 pmKota Kinabalu
Apr 12
BKI9:20 pmKota Kinabalu
23h 35m
1 stop
MNL8:55 pmManila Ninoy Aquino Intl
$265
Royal Brunei Airlines
May 1
MNL9:45 pmManila Ninoy Aquino Intl
18h 25m
1 stop
BKI4:10 pmKota Kinabalu
May 8
BKI8:50 amKota Kinabalu
12h 05m
1 stop
MNL8:55 pmManila Ninoy Aquino Intl
$267
Royal Brunei Airlines
Apr 3
MNL9:45 pmManila Ninoy Aquino Intl
18h 25m
1 stop
BKI4:10 pmKota Kinabalu
Apr 10
BKI9:45 pmKota Kinabalu
16h 25m
1 stop
MNL2:10 pmManila Ninoy Aquino Intl
$268

Scoot flights from Manila to Kota Kinabalu

Our best Scoot deals on Manila to Kota Kinabalu flight tickets
Scoot
Aug 10
MNL6:55 amManila Ninoy Aquino Intl
28h 20m
1 stop
BKI11:15 amKota Kinabalu
Aug 13
BKI12:15 pmKota Kinabalu
17h 35m
1 stop
MNL5:50 amManila Ninoy Aquino Intl
$230
Scoot
Aug 10
MNL6:55 amManila Ninoy Aquino Intl
28h 20m
1 stop
BKI11:15 amKota Kinabalu
Aug 13
BKI12:15 pmKota Kinabalu
17h 35m
1 stop
MNL5:50 amManila Ninoy Aquino Intl
$233
Scoot
May 4
MNL7:40 pmManila Ninoy Aquino Intl
15h 35m
1 stop
BKI11:15 amKota Kinabalu
May 9
BKI8:45 pmKota Kinabalu
9h 05m
1 stop
MNL5:50 amManila Ninoy Aquino Intl
$246

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 March 18, 2026.
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

Cheapest round-trip
Quickest round-trip

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 4/12

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Sun 5/10

1:45 am-3:55 am

Nonstop2h 10m

$99

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Mon 8/10

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Wed 8/12

1:45 am-3:55 am

Nonstop2h 10m

$104

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Mon 8/10

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Wed 8/12

1:45 am-3:55 am

Nonstop2h 10m

$105

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 6/17

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Fri 6/19

1:45 am-3:55 am

Nonstop2h 10m

$107

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Mon 5/4

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Fri 5/8

1:45 am-3:55 am

Nonstop2h 10m

$117

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 8/23

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Fri 8/28

1:45 am-3:55 am

Nonstop2h 10m

$123

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Fri 4/17

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Sun 4/19

1:45 am-3:55 am

Nonstop2h 10m

$129

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Wed 5/27

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Fri 5/29

1:45 am-3:55 am

Nonstop2h 10m

$154

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Fri 4/3

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Sun 4/5

1:45 am-3:55 am

Nonstop2h 10m

$166

ManilaKota Kinabalu

MNL - BKI

MNLBKI

Manila Ninoy Aquino Intl

Sun 4/12

11:10 pm-1:20 am

Nonstop2h 10m

Kota Kinabalu

Mon 5/11

8:30 pm-5:50 am

1 stop9h 20m

$188

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 typical price of a round-trip flight between Manila and Kota Kinabalu?

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 $88.

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 $139. 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 $101. 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 $107. 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 $108 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 $90 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 March 2026, prices for Manila to Kota Kinabalu flights are approximately 16% 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

$101

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 $101
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 in Kota Kinabalu. From Manila there are direct flights to Kota Kinabalu (BKI).
  • 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
6.8
125 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 4 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 $102. Our users have rated Philippines AirAsia at 6.8/10.

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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