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Cheap flights from Tokyo to Kota Kinabalu from RM 689

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 27/6. Fares are subject to change and may not be available on all flights or dates of travel.
TYO — BKI
3 May — 10 May1
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 April 2026.

Sun 12/723:50
HND
-
BKI
1 stop13h 05m
Multiple Airlines
Sat 18/706:00
BKI
-
HND
1 stop15h 35m
Multiple Airlines
Deal found 30/3RM 988
Wed 13/508:20
NRT
-
BKI
1 stop12h 10m
Scoot
Wed 20/509:50
BKI
-
NRT
1 stop20h 15m
Scoot
Deal found 31/3RM 1,153
Tue 1/921:15
NRT
-
BKI
2 stops12h 35m
Scoot
Tue 15/912:15
BKI
-
NRT
1 stop17h 50m
Scoot
Deal found 31/3RM 1,189
Mon 31/802:20
HND
-
BKI
1 stop31h 30m
Scoot
Tue 15/912:15
BKI
-
HND
1 stop11h 50m
Scoot
Deal found 31/3RM 1,221
Fri 16/1002:20
HND
-
BKI
1 stop18h 25m
Scoot
Tue 20/1012:15
BKI
-
HND
1 stop11h 50m
Scoot
Deal found 29/3RM 1,294
Sun 12/713:45
NRT
-
BKI
1 stop12h 35m
Multiple Airlines
Fri 17/701:45
BKI
-
NRT
1 stop15h 15m
Multiple Airlines
Deal found 30/3RM 1,334
Wed 2/911:10
NRT
-
BKI
1 stop15h 10m
Multiple Airlines
Wed 16/901:15
BKI
-
NRT
1 stop12h 30m
Multiple Airlines
Deal found 31/3RM 1,358
Fri 4/911:10
NRT
-
BKI
1 stop15h 10m
Multiple Airlines
Wed 16/901:15
BKI
-
NRT
1 stop12h 30m
Multiple Airlines
Deal found 31/3RM 1,371
Thu 14/515:45
NRT
-
BKI
1 stop9h 45m
HK Express
Wed 20/501:15
BKI
-
NRT
1 stop16h 10m
HK Express
Deal found 29/3RM 1,375
Fri 4/911:10
NRT
-
BKI
1 stop15h 10m
Multiple Airlines
Sun 13/901:15
BKI
-
NRT
1 stop12h 30m
Multiple Airlines
Deal found 31/3RM 1,383
Fri 15/502:20
HND
-
BKI
1 stop18h 25m
Scoot
Sat 23/520:45
BKI
-
HND
1 stop27h 20m
Scoot
Deal found 1/4RM 1,419
Wed 13/506:35
HND
-
BKI
1 stop18h 55m
HK Express
Tue 19/501:15
BKI
-
HND
1 stop20h 40m
HK Express
Deal found 31/3RM 1,508

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 April 2026.

Round-trip from

RM 988

One-way from

RM 689
12/7-18/7
  • 12/7-18/7
  • 2 total stops
  • 28h 40m total
  • Tokyo to Kota Kinabalu
Search Deals
Scoot
  • Scoot
  • 27/6
  • 1 total stop
  • 31h 30m 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 April 2026.
Use the filters below to find and compare flights from Tokyo to Kota Kinabalu that are best for you.

Fly from

Fly to

Route

Departure

Return

Price

Cheapest return flight

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Wed 13/5

08:20-19:30

1 stop12h 10m

Kota Kinabalu

Wed 20/5

20:30-20:00

2 stops22h 30m

RM 1,217

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Sun 12/7

13:45-01:20

1 stop12h 35m

Kota Kinabalu

Fri 17/7

01:45-18:00

1 stop15h 15m

RM 1,334

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Thu 14/5

15:45-00:30

1 stop9h 45m

Kota Kinabalu

Wed 20/5

01:15-18:25

1 stop16h 10m

RM 1,375

TokyoKota Kinabalu

HND - BKI

HNDBKI

Tokyo Haneda

Thu 14/5

06:35-00:30

1 stop18h 55m

Kota Kinabalu

Thu 21/5

11:45-01:00

1 stop12h 15m

RM 1,701

TokyoKota Kinabalu

HND - BKI

HNDBKI

Tokyo Haneda

Tue 12/5

02:10-12:30

1 stop11h 20m

Kota Kinabalu

Wed 20/5

20:30-01:00

2 stops27h 30m

RM 1,709

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Sun 12/7

08:20-08:50

1 stop25h 30m

Kota Kinabalu

Sat 18/7

20:45-11:15

2 stops13h 30m

RM 1,750

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Sun 17/5

11:45-20:10

1 stop9h 25m

Kota Kinabalu

Sun 24/5

07:05-07:30

1 stop23h 25m

RM 1,778

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Sun 17/5

08:20-08:50

1 stop25h 30m

Kota Kinabalu

Sun 24/5

12:15-20:00

2 stops30h 45m

RM 1,883

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Tue 1/9

18:30-00:30

1 stop31h 00m

Kota Kinabalu

Fri 11/9

01:15-14:30

1 stop12h 15m

RM 2,060

TokyoKota Kinabalu

NRT - BKI

NRTBKI

Tokyo Narita

Wed 13/5

22:00-00:30

1 stop27h 30m

Kota Kinabalu

Sat 16/5

01:15-06:50

1 stop28h 35m

RM 2,064

Flights are sorted by cheapest return flights first.

Deals found on 31/3

Showing 1-10 of 23 resultsSorted by cheapest first
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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.

Kuala Lumpur (KUL) – chosen by Cheapflights users on 63% 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 1,412.

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 53m.

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 in the morning 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 Saturday 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 Scoot, HK Express, and Cathay Pacific fly from Tokyo to Kota Kinabalu in about 9h 10m. The time it takes to get you to your destination can typically vary by up to 3h. Tokyo and Kota Kinabalu are separated by a distance of 4088 km. Both multi-stop and direct flights can be found to your destination and back.

  • 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

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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

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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.

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