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Cheap Flights from Tokyo to Kota Kinabalu

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Flight deals from Tokyo to Kota Kinabalu Airport

Looking for a cheap last-minute deal or the best return flight from Tokyo to Kota Kinabalu Airport? If you want to travel next month, return fares start from $617. Find the lowest prices on one-way and return tickets right here.
Kota Kinabalu.$411 per passenger.Departing Sat, 11 Jul, returning Sat, 8 Aug.Return flight with AirAsia X and AirAsia.Outbound indirect flight with AirAsia X, departs from Tokyo Haneda on Sat, 11 Jul, arriving in Kota Kinabalu.Inbound indirect flight with AirAsia, departs from Kota Kinabalu on Sat, 8 Aug, arriving in Tokyo Haneda.Price includes taxes and charges.From $411, select.
Kota Kinabalu.$416 per passenger.Departing Sun, 5 Jul, returning Wed, 8 Jul.Return flight with AirAsia X and AirAsia.Outbound indirect flight with AirAsia X, departs from Tokyo Haneda on Sun, 5 Jul, arriving in Kota Kinabalu.Inbound indirect flight with AirAsia, departs from Kota Kinabalu on Wed, 8 Jul, arriving in Tokyo Haneda.Price includes taxes and charges.From $416, select.
Kota Kinabalu.$416 per passenger.Departing Sat, 20 Jun, returning Mon, 22 Jun.Return flight with AirAsia X and AirAsia.Outbound indirect flight with AirAsia X, departs from Tokyo Haneda on Sat, 20 Jun, arriving in Kota Kinabalu.Inbound indirect flight with AirAsia, departs from Kota Kinabalu on Mon, 22 Jun, arriving in Tokyo Haneda.Price includes taxes and charges.From $416, select.
Kota Kinabalu.$486 per passenger.Departing Fri, 28 Aug, returning Mon, 31 Aug.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Haneda on Fri, 28 Aug, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Mon, 31 Aug, arriving in Tokyo Haneda.Price includes taxes and charges.From $486, select.
Kota Kinabalu.$496 per passenger.Departing Tue, 1 Sep, returning Sat, 5 Sep.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Narita on Tue, 1 Sep, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Sat, 5 Sep, arriving in Tokyo Narita.Price includes taxes and charges.From $496, select.
Kota Kinabalu.$498 per passenger.Departing Tue, 12 May, returning Mon, 18 May.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Narita on Tue, 12 May, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Mon, 18 May, arriving in Tokyo Narita.Price includes taxes and charges.From $498, select.
Kota Kinabalu.$502 per passenger.Departing Sun, 10 May, returning Sun, 7 Jun.Return flight with AirAsia X and AirAsia.Outbound indirect flight with AirAsia X, departs from Tokyo Haneda on Sun, 10 May, arriving in Kota Kinabalu.Inbound indirect flight with AirAsia, departs from Kota Kinabalu on Sun, 7 Jun, arriving in Tokyo Haneda.Price includes taxes and charges.From $502, select.
Kota Kinabalu.$532 per passenger.Departing Mon, 29 Jun, returning Mon, 13 Jul.Return flight with AirAsia X and AirAsia.Outbound indirect flight with AirAsia X, departs from Tokyo Haneda on Mon, 29 Jun, arriving in Kota Kinabalu.Inbound indirect flight with AirAsia, departs from Kota Kinabalu on Mon, 13 Jul, arriving in Tokyo Haneda.Price includes taxes and charges.From $532, select.
Kota Kinabalu.$550 per passenger.Departing Wed, 7 Oct, returning Sun, 11 Oct.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Haneda on Wed, 7 Oct, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Sun, 11 Oct, arriving in Tokyo Haneda.Price includes taxes and charges.From $550, select.
Kota Kinabalu.$574 per passenger.Departing Sun, 30 Aug, returning Thu, 10 Sep.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Haneda on Sun, 30 Aug, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Thu, 10 Sep, arriving in Tokyo Haneda.Price includes taxes and charges.From $574, select.
Kota Kinabalu.$617 per passenger.Departing Tue, 21 Apr, returning Fri, 24 Apr.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Narita on Tue, 21 Apr, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Fri, 24 Apr, arriving in Tokyo Narita.Price includes taxes and charges.From $617, select.
Kota Kinabalu.$626 per passenger.Departing Mon, 2 Nov, returning Fri, 6 Nov.Return flight with China Southern.Outbound indirect flight with China Southern, departs from Tokyo Narita on Mon, 2 Nov, arriving in Kota Kinabalu.Inbound indirect flight with China Southern, departs from Kota Kinabalu on Fri, 6 Nov, arriving in Tokyo Haneda.Price includes taxes and charges.From $626, select.
Kota Kinabalu.$628 per passenger.Departing Wed, 9 Dec, returning Sat, 12 Dec.Return flight with China Southern.Outbound indirect flight with China Southern, departs from Tokyo Narita on Wed, 9 Dec, arriving in Kota Kinabalu.Inbound indirect flight with China Southern, departs from Kota Kinabalu on Sat, 12 Dec, arriving in Tokyo Haneda.Price includes taxes and charges.From $628, select.
Kota Kinabalu.$668 per passenger.Departing Tue, 21 Apr, returning Thu, 7 May.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Narita on Tue, 21 Apr, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Thu, 7 May, arriving in Tokyo Narita.Price includes taxes and charges.From $668, select.
Kota Kinabalu.$705 per passenger.Departing Sun, 27 Sep, returning Sat, 3 Oct.Return flight with Scoot.Outbound indirect flight with Scoot, departs from Tokyo Narita on Sun, 27 Sep, arriving in Kota Kinabalu.Inbound indirect flight with Scoot, departs from Kota Kinabalu on Sat, 3 Oct, arriving in Tokyo Narita.Price includes taxes and charges.From $705, select.
Kota Kinabalu.$759 per passenger.Departing Wed, 10 Feb, returning Sat, 13 Feb.Return flight with Royal Brunei .Outbound indirect flight with Royal Brunei , departs from Tokyo Narita on Wed, 10 Feb, arriving in Kota Kinabalu.Inbound indirect flight with Royal Brunei , departs from Kota Kinabalu on Sat, 13 Feb, arriving in Tokyo Narita.Price includes taxes and charges.From $759, select.

Find the cheapest month to fly from Tokyo to Kota Kinabalu

We’re always keeping an eye on fares, so you can find the best one in seconds. It looks like Tokyo to Kota Kinabalu flights are currently cheapest in June.
Mar
from $1,370
Apr
from $617
May
from $498
Jun
from $416
Jul
from $416
Aug
from $486
Sep
from $496
Oct
from $550
Nov
from $626
Dec
from $628
Jan
from $1,227
Feb
from $759

Tokyo to Kota Kinabalu: Alternative routes

Compare routes from Tokyo to Kota Kinabalu below. You may find an airport to fly into that's cheaper, faster, or easier than Kota Kinabalu.

Kota Kinabalu

6km from central Kota Kinabalu
ClosestCheapest
from $411
Search flights

Tokyo to Kota Kinabalu: Flight information

The things to know before you go.
Cheapest flight found$411
Cheapest month to flyJuly

Check out these Kota Kinabalu hotels

Ready to plan your stay? Other travellers rate these Kota Kinabalu hotels for cleanliness, service and location.
The Voyagers Home Borneo Kota Kinabalu
0.55 km from city centre
$374
Per night
A Residence
1.08 km from city centre
$76
Per night
Bay Premier Suites by Ssvc
1.88 km from city centre
$37
Per night
The Voyagers Home Borneo Kota Kinabalu
0.55 km from city centre
$374
Per night
A Residence
1.08 km from city centre
$76
Per night
Bay Premier Suites by Ssvc
1.88 km from city centre
$37
Per night
Explore top-rated hotels

Finding cheap flights from Tokyo to Kota Kinabalu: Frequently asked questions

The best price we found for a return flight from Tokyo to Kota Kinabalu is $411. This is an estimate based on information collected from different airlines and travel providers over the last 4 days and is subject to change and availability.
Currently, there are no airlines that fly direct from Tokyo to Kota Kinabalu. But we found flights with one stop from $411.
As of March 2026, there are no flights flying from Tokyo to Kota Kinabalu.
The cheapest month to fly from Tokyo to Kota Kinabalu is usually July.
After crunching the numbers on our flight calendar, we found that it is currently cheapest to fly from Tokyo to Kota Kinabalu Airport on Saturday, 11 July 2026.
No airlines currently offer direct flights between Tokyo and Kota Kinabalu Airport. Most routes have one or more stops.
We show every price from over 1,200 airlines and travel agents, comparing them all so you don’t have to. If you know you want to fly to Kota Kinabalu but you’re not ready to book, set up a Price Alert. We’ll track prices for you, and let you know when they rise or fall.
We crunched all the numbers in our flight calendar and it looks like the cheapest time to book a flight to Kota Kinabalu is around 40 days in advance, so don’t leave your flight to the last minute.
The cheapest airline that flies to Kota Kinabalu is AirAsia X .

Travelling from Tokyo to Kota Kinabalu International Airport (BKI): What you need to know

  • Planning your holiday starts with figuring out where you'll leave from in Tokyo. Tokyo Narita International Airport (NRT) is the city's main airport, so check out your options for booking a flight from Tokyo to Kota Kinabalu International Airport (BKI) leaving from here.

  • The timezone in Kota Kinabalu is UTC+8, which is one hour behind Tokyo. Kota Kinabalu International Airport is located in Kota Kinabalu.

  • Give yourself enough time to get on your flight from Tokyo to BKI. A good rule of thumb is to arrive at least two hours before international departures and an hour ahead for domestic flights.

  • Travelling during a peak month like March? School holidays and other high seasons can lead to longer lines and delays at security. Play things extra safe and arrive up to four hours before an international flight and two hours before a domestic departure.

Airports in Tokyo

Tokyo Haneda International Airport (HND)

  • Consider adding a stopover to find cheap flights from Tokyo to BKI. Just uncheck 'Direct flights only' when browsing departures from Tokyo Haneda International Airport (HND). Break up your trip (and maybe get a better deal) by stopping at one of these popular airports:

    • Guangzhou Baiyun International Airport (CAN)

    • Shanghai Pudong International Airport (PVG)

    • Hong Kong International Airport (HKG)

  • Located around 19 kilometres from central Tokyo, HND can be reached in about 25 minutes by car, depending on traffic. The journey on public transport takes roughly 30 minutes.

  • Catching an early flight from Tokyo to Kota Kinabalu International Airport? Avoid the last-minute rush to the terminal (and get a little more snooze time) by staying at one of these hotels near Tokyo Haneda International Airport:

  • When it comes to the on-time performance of Tokyo Haneda International Airport, 78% of flights complete their journey on time.

  • You'll find HND at 3丁目 Hanedakuko, Ota.

Tokyo Narita International Airport (NRT)

  • Looking to fly out of Tokyo Narita International Airport (NRT)? Direct Tokyo to Kota Kinabalu International Airport (BKI) plane tickets are available from this popular hub.

  • Catch your direct flight from Tokyo to BKI with Malaysia Airlines. This is one of the main carriers flying this route out of NRT.

  • On the NRT to BKI route, Malaysia Airlines is the preferred choice of many.

  • Get the most out of your holiday with a stopover on your flight from Tokyo to Kota Kinabalu International Airport. Here's where you can connect between Tokyo Narita International Airport and BKI:

    • Shanghai Pudong International Airport (PVG)

    • Seoul Incheon International Airport (ICN)

    • Hong Kong International Airport (HKG)

  • Using public transport, you can travel from central Tokyo to NRT in about 1 hour. The terminal is roughly 56 kilometres away, and making the trip by car will take approximately 1 hour 5 minutes.

  • Get your holiday started early with an additional night away from home. Before catching your Tokyo to BKI flight, stay in one of these hotels close to Tokyo Narita International Airport:

  • 73% of flights taking off from Tokyo Narita International Airport arrive according to schedule.

  • You'll find NRT at 成田空港第2PTB(バス), Narita.

About Kota Kinabalu International Airport (BKI)

Getting from Kota Kinabalu International Airport (BKI) to central Kota Kinabalu

  • Kota Kinabalu International Airport to the centre of Kota Kinabalu is around 8 kilometres. If you're renting a car or taking a taxi, plan ahead to make your trip as smooth as possible. Journey times vary depending on the time of day and traffic conditions.

  • Travelling by public transport will take you roughly 35 minutes.

How to find the cheapest flights from Tokyo to Kota Kinabalu International Airport (BKI)

  • $203 is currently the lowest price for a one-way ticket from Tokyo to Kota Kinabalu International Airport. A return flight starts from $411. These fares can change depending on demand.

  • To pick up cheap flights from Tokyo to BKI, book early. Airlines typically offer lower fares when flights first go on sale.

  • The 'Whole month' search tool will show you the cheapest Tokyo to Kota Kinabalu International Airport tickets across every month. It's a great way to find a bargain if your dates aren't set in stone.

  • Stay on top of deals for plane tickets from Tokyo to BKI by setting up a Price Alert. We'll send you an email or notification on the app when a lower fare becomes available.

  • Save on your flight from Tokyo to Kota Kinabalu International Airport by using the search filters. Select your ideal times, number of stops and airlines, then sort the results by 'Cheapest' for the best deals.

The best time to fly from Tokyo to Kota Kinabalu International Airport (BKI)

  • It's time to decide your travel dates for your flight from Tokyo to Kota Kinabalu International Airport (BKI). February is the busiest month to visit Kota Kinabalu. If you like your getaways a little more chill, think about going in December.

  • Lock in a Tokyo to BKI plane ticket departing in May if you want to experience the city during its warmest month. Expect temperatures in Kota Kinabalu to range from 24ºC to 31ºC.

  • If you like travelling in cooler conditions, search for a cheap ticket from Tokyo to Kota Kinabalu International Airport in February when temperatures are between 23ºC and 29ºC.

More about Kota Kinabalu

  • When it comes to looking for somewhere to rest your head, you'll find the best places to stay in Kota Kinabalu right here. Browse these options as soon as you've locked in your flight from Tokyo to Kota Kinabalu International Airport:

  • All great adventures should include some sightseeing. Tunku Abdul Rahman National Park, Danum Valley Conservation Area (DVCA) and Manukan Island are must-do's during your Kota Kinabalu adventure.

Explore more of Malaysia

  • Kota Kinabalu is always a good idea, but there are so many other corners of Malaysia waiting to be discovered. About 225 kilometres east of Kota Kinabalu, a visit to Sandakan will keep your itinerary busy. Start with leading sights like Sepilok Orangutan Rehabilitation Centre, Sun Bear Conservation Centre, Sepilok and Sandakan Rainforest Park.

  • If you're interested in discovering another side of Malaysia, head for Tawau, roughly 274 kilometres southeast of Kota Kinabalu. Hot Springs Tawau, Teck Guan Cocoa Museum and Batu payung are the start of reasons to visit.

More travel options

Plan the rest of your trip from Tokyo to Kota Kinabalu

Prices shown on this page are estimated lowest prices only. Found in the last 45 days.