Find flights
When to book
FAQs

Cheap flights from Tokyo to Kota Kinabalu from RM 646

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 25/5. Fares are subject to change and may not be available on all flights or dates of travel.
TYO — BKI
5 Mar — 12 Mar1
1 adult
1 adult, Economy, 0 bags

Cheap flight deals from Tokyo to Kota Kinabalu

Enter your travel dates to find the best prices.

Cheapest flights from Tokyo to Kota Kinabalu
Explore the most affordable flight options available from Tokyo to Kota Kinabalu. Find the lowest fares from popular airlines and budget airlines, with prices last updated on 3 February 2026.

Sat 21/320:05
NRT
-
BKI
1 stop29h 25m
HK Express
Wed 25/301:30
BKI
-
NRT
1 stop15h 35m
HK Express
Deal found 2/2RM 1,312
Wed 18/320:55
NRT
-
BKI
1 stop28h 35m
HK Express
Tue 24/301:30
BKI
-
NRT
1 stop16h 35m
HK Express
Deal found 1/2RM 1,402
Wed 6/508:30
NRT
-
BKI
1 stop12h 00m
Multiple Airlines
Thu 7/501:15
BKI
-
NRT
1 stop17h 30m
Multiple Airlines
Deal found 2/2RM 1,414
Mon 2/315:30
NRT
-
BKI
1 stop27h 30m
XiamenAir
Wed 11/319:00
BKI
-
NRT
1 stop17h 40m
XiamenAir
Deal found 2/2RM 1,426
Mon 27/415:45
NRT
-
BKI
1 stop9h 45m
HK Express
Thu 7/501:15
BKI
-
NRT
1 stop17h 30m
HK Express
Deal found 2/2RM 1,434
Sat 21/319:00
NRT
-
BKI
1 stop30h 30m
HK Express
Tue 24/301:30
BKI
-
NRT
1 stop16h 35m
HK Express
Deal found 1/2RM 1,446
Sat 21/306:35
HND
-
BKI
1 stop18h 55m
HK Express
Wed 25/301:30
BKI
-
HND
1 stop22h 15m
HK Express
Deal found 2/2RM 1,454
Tue 28/408:30
NRT
-
BKI
1 stop25h 15m
Scoot
Thu 7/512:15
BKI
-
NRT
1 stop18h 00m
Scoot
Deal found 2/2RM 1,457
Mon 27/415:45
NRT
-
BKI
1 stop9h 45m
HK Express
Sat 2/501:15
BKI
-
NRT
1 stop17h 30m
HK Express
Deal found 2/2RM 1,481
Mon 2/319:30
NRT
-
BKI
2 stops22h 15m
Multiple Airlines
Wed 11/309:20
BKI
-
NRT
1 stop9h 40m
Multiple Airlines
Deal found 2/2RM 1,489
Tue 28/408:30
NRT
-
BKI
1 stop25h 15m
Scoot
Fri 8/522:00
BKI
-
NRT
2 stops21h 00m
Scoot
Deal found 2/2RM 1,493
Wed 18/306:35
HND
-
BKI
1 stop18h 55m
HK Express
Tue 24/301:30
BKI
-
HND
1 stop22h 15m
HK Express
Deal found 1/2RM 1,501

Find flight deals from Tokyo to Kota Kinabalu

Discover tips and strategies to find the most affordable flight options for your journey from Tokyo (TYO) 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 3 February 2026.

Round-trip from

RM 1,402

One-way from

RM 646
HK Express
  • HK Express
  • 18/3-24/3
  • 2 total stops
  • 45h 10m total
  • Tokyo to Kota Kinabalu
Search Deals
Scoot
  • Scoot
  • 25/5
  • 1 total stop
  • 12h 00m total
  • Tokyo to Kota Kinabalu
Search Deals

Cheapflights Fare Finder

 
Customise your flight search to find flights from Tokyo 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 407,431 searches. Data last updated 3 February 2026.
Use the filters below to find and compare flights from Tokyo to Kota Kinabalu that are best for you.

Fly from

Tokyo

Fly to

Kota Kinabalu

Route

Departure

Return

Price

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Sat 21/3

20:05-00:30

1 stop29h 25m

Kota Kinabalu

Wed 25/3

01:30-18:05

1 stop15h 35m

RM 1,312

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Wed 18/3

20:55-00:30

1 stop28h 35m

Kota Kinabalu

Tue 24/3

01:30-19:05

1 stop16h 35m

RM 1,402

TokyoKota Kinabalu

HND - BKI

HNDBKI

Tokyo Haneda

Sat 21/3

06:35-00:30

1 stop18h 55m

Kota Kinabalu

Wed 25/3

01:30-00:45

1 stop22h 15m

RM 1,454

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Wed 1/7

10:25-22:15

1 stop12h 50m

Kota Kinabalu

Wed 15/7

16:30-20:50

1 stop27h 20m

RM 1,489

TokyoKota Kinabalu

HND - BKI

HNDBKI

Tokyo Haneda

Wed 18/3

06:35-00:30

1 stop18h 55m

Kota Kinabalu

Tue 24/3

01:30-00:45

1 stop22h 15m

RM 1,501

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Tue 28/4

08:30-08:45

1 stop25h 15m

Kota Kinabalu

Fri 8/5

22:00-07:15

1 stop32h 15m

RM 1,520

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Wed 18/3

10:55-15:55

2 stops30h 00m

Kota Kinabalu

Tue 24/3

01:30-20:00

1 stop17h 30m

RM 1,717

TokyoKota Kinabalu

HND - BKI

HNDBKI

Tokyo Haneda

Wed 1/7

23:50-10:30

1 stop11h 40m

Kota Kinabalu

Wed 15/7

09:05-22:35

1 stop12h 30m

RM 1,788

TokyoKota Kinabalu

HND - BKI

HNDBKI

Tokyo Haneda

Mon 27/4

02:15-08:45

1 stop31h 30m

Kota Kinabalu

Fri 8/5

22:00-01:00

1 stop26h 00m

RM 1,816

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Sat 21/3

07:45-08:00

2 stops25h 15m

Kota Kinabalu

Wed 25/3

01:30-18:05

1 stop15h 35m

RM 1,816

Flights are sorted by cheapest return flights first.

Deals found on 1/2

Showing 1-10 of 40 results
1
2
3
4

Best time to book a flight from Tokyo to Kota Kinabalu

Have a flexible travel schedule? Discover the best time to fly to Kota Kinabalu from Tokyo with our price prediction graph.
Estimated return 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 Tokyo to Kota Kinabalu

What’s the top stopover airport for flights from Tokyo to Kota Kinabalu?

Share of one-stop return flights from Tokyo to Kota Kinabalu chosen by Cheapflights users in the past 12 months, using the same stopover each way.

Incheon (ICN) – chosen by Cheapflights users on 75% of one-stop itineraries from Tokyo to Kota Kinabalu on Cheapflights.

What’s the cheapest stopover airport for flights from Tokyo to Kota Kinabalu?

Average return fare for one-stop flights from Tokyo to Kota Kinabalu, chosen by Cheapflights users in the past 12 months, with the same stopover each way.

Incheon (ICN) is the most affordable one-stop option, with an average return flight price of RM 1,380.

What’s the fastest stopover option from Tokyo to Kota Kinabalu?

Shortest average travel time for one-stop one-way flights from Tokyo to Kota Kinabalu, based on itineraries clicked by Cheapflights users over the past 12 months, grouped by stopover airport.

Flights via Incheon (ICN) have the shortest average one-way travel time for one-stop routes: 11h 35m.

Which airport typically offers the quickest stopover for flights from Tokyo to Kota Kinabalu?

Average stopover duration for one-stop one-way flights from Tokyo to Kota Kinabalu, chosen by Cheapflights users in the last 12 months, grouped by stopover airport.

Flights via Kuala Lumpur (KUL) offer the fastest connection on this route, with an average stopover time of 2h 25m.

How often are flights from Tokyo to Kota Kinabalu delayed?

About 0% of weekly flights between Tokyo and Kota Kinabalu have experienced delays in the past year, with the average delay time being 0 minutes.

What is the most punctual flight time for Tokyo to Kota Kinabalu flights?

Historically, flights departing at night are less likely to be delayed, whereas flights leaving at night tend to experience delays more often.

What day of the week experiences the fewest flight delays on this route?

Tuesday tends to have the lowest number of delays on this route, whereas Friday has historically faced a higher average of delays compared to other days of the week.

Related info for your journey

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

  • What airport do you fly into for flights to Kota Kinabalu from Tokyo?

    If you book a flight to Kota Kinabalu from Tokyo, you will be flying to Kota Kinabalu, which is the city’s only airport. Kota Kinabalu (BKI) is located 5.8 km from the centre of Kota Kinabalu. There are 0 flights from Tokyo to Kota Kinabalu per day from 0 different airlines.

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

    Airlines like HK Express, Batik Air, and Scoot fly from Tokyo to Kota Kinabalu in about 12h 50m. The time it takes to get you to your destination can typically vary by up to 16h 35m. Tokyo and Kota Kinabalu are separated by a distance of 4142 km. Both multi-stop and direct flights can be found to your destination and back.

  • What are the cheapest airlines to fly from Tokyo to Kota Kinabalu one-way?

    To fly one-way, consider booking your trip with Scoot, which is currently one of the cheapest options available, starting at RM 575. Philippines AirAsia flights start at RM 623 while deals on Jeju Air start at RM 721 one-way.

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

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

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

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

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

    Yes. Cheapflights offers flight deals from Tokyo 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.

See more FAQs

Browse thousands of different options on Cheapflights for your next trip

Toggle through the tabs below to find thousands of options on Cheapflights for your next trip.

Alternative routes for Tokyo to Kota Kinabalu

See prices for flight routes from nearby airports that may be better suited for you.
Narita to Kota Kinabalu flights

Fly with Cheapflights

Find the best flight deals on Cheapflights, where travellers can enjoy low prices and a wide availability of flights to their desired destinations.

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

Cheapflights helps you search for flights from Tokyo to Kota Kinabalu via 900+ travel sites so you don’t have to. After performing a flight search, users can also filter their flight selection by filtering for price, number of stops, airlines, and so on.

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

Millions of users choose and trust Cheapflights to book the best flight deals from Tokyo to Kota Kinabalu for free. We help you search and compare prices from hundreds of airlines for the right flight just for you.

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

Cheapflights does show flights with no change fees to all users. To see these options for flights from Tokyo to Kota Kinabalu, users can toggle the no change fees filter when performing a flight search.

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

Not ready to book yet? You can track prices for flights from Tokyo to Kota Kinabalu on Cheapflights with our Price Alert feature and get notified when better prices are available.

100% Free

Cheapflights is completely free to use, so you can start saving the moment you arrive.

Book With Flexibility

Our users can plan ahead with confidence and find flights with no change fees.

Travel Smart

Millions of people come to us for their flight needs every year. We help make travel planning easy by providing useful insights and data-driven graphs that can inform your decisions.