Cheap Flights from Tokyo to El Nido from RM1,540

Compare Tokyo to El Nido flight deals

Find the cheapest month or even day of the year to fly to El Nido

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Flight deals from Tokyo to El Nido

Looking for a cheap last-minute deal or the best return flight from Tokyo to El Nido? Find the lowest prices on one-way and return tickets right here.

El Nido.RM1,540 per passenger.Departing Fri, 5 Sep, returning Sat, 13 Sep.Return flight with Zipair and Cebgo.Outbound indirect flight with Zipair, departs from Tokyo Narita on Fri, 5 Sep, arriving in El Nido.Inbound indirect flight with Cebgo, departs from El Nido on Sat, 13 Sep, arriving in Tokyo Narita.Price includes taxes and charges.From RM1,540, select.

El Nido.RM1,607 per passenger.Departing Mon, 4 Aug, returning Sat, 9 Aug.Return flight with Philippines AirAsia and Cebgo.Outbound indirect flight with Philippines AirAsia, departs from Tokyo Narita on Mon, 4 Aug, arriving in El Nido.Inbound indirect flight with Cebgo, departs from El Nido on Sat, 9 Aug, arriving in Tokyo Narita.Price includes taxes and charges.From RM1,607, select.

El Nido.RM1,634 per passenger.Departing Wed, 7 May, returning Wed, 14 May.Return flight with Cebu Pacific and Cebgo.Outbound indirect flight with Cebu Pacific, departs from Tokyo Narita on Wed, 7 May, arriving in El Nido.Inbound indirect flight with Cebgo, departs from El Nido on Wed, 14 May, arriving in Tokyo Narita.Price includes taxes and charges.From RM1,634, select.

El Nido.RM1,641 per passenger.Departing Wed, 23 Jul, returning Sun, 27 Jul.Return flight with Cebu Pacific and Cebgo.Outbound indirect flight with Cebu Pacific, departs from Tokyo Narita on Wed, 23 Jul, arriving in El Nido.Inbound indirect flight with Cebgo, departs from El Nido on Sun, 27 Jul, arriving in Tokyo Narita.Price includes taxes and charges.From RM1,641, select.

El Nido.RM1,683 per passenger.Departing Sun, 1 Jun, returning Fri, 13 Jun.Return flight with Cebu Pacific and Cebgo.Outbound indirect flight with Cebu Pacific, departs from Tokyo Narita on Sun, 1 Jun, arriving in El Nido.Inbound indirect flight with Cebgo, departs from El Nido on Fri, 13 Jun, arriving in Tokyo Narita.Price includes taxes and charges.From RM1,683, select.

El Nido.RM1,930 per passenger.Departing Sun, 30 Mar, returning Fri, 4 Apr.Return flight with Jetstar and Air Swift.Outbound indirect flight with Jetstar, departs from Tokyo Narita on Sun, 30 Mar, arriving in El Nido.Inbound indirect flight with Air Swift, departs from El Nido on Fri, 4 Apr, arriving in Tokyo Narita.Price includes taxes and charges.From RM1,930, select.

El Nido.RM2,068 per passenger.Departing Wed, 2 Apr, returning Tue, 8 Apr.Return flight with Jetstar and Cebgo.Outbound indirect flight with Jetstar, departs from Tokyo Narita on Wed, 2 Apr, arriving in El Nido.Inbound indirect flight with Cebgo, departs from El Nido on Tue, 8 Apr, arriving in Tokyo Narita.Price includes taxes and charges.From RM2,068, select.

El Nido.RM2,088 per passenger.Departing Mon, 24 Mar, returning Sun, 30 Mar.Return flight with Cebu Pacific and Cebgo.Outbound indirect flight with Cebu Pacific, departs from Tokyo Narita on Mon, 24 Mar, arriving in El Nido.Inbound indirect flight with Cebgo, departs from El Nido on Sun, 30 Mar, arriving in Tokyo Narita.Price includes taxes and charges.From RM2,088, select.

Find the cheapest month to fly from Tokyo to El Nido

We’re always keeping an eye on fares, so you can find the best one in seconds. It looks like Tokyo to El Nido flights are currently cheapest in September.

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Tokyo to El Nido: Alternative routes

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

Tokyo to El Nido: Flight information

The things to know before you go.

Cheapest flight found	RM1,540
Cheapest month to fly	September

Finding cheap flights from Tokyo to El Nido: Frequently asked questions

How much are return flights from Tokyo to El Nido?

The best price we found for a return flight from Tokyo to El Nido is RM1,540. 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.

Which airlines fly direct from Tokyo to El Nido?

Currently, there are no airlines that fly direct from Tokyo to El Nido. But we found flights with one stop from RM1,540.

How many flights are there a week from Tokyo to El Nido?

As of February 2025, there are no flights flying from Tokyo to El Nido.

When is the cheapest time to fly from Tokyo to El Nido?

The cheapest month to fly from Tokyo to El Nido is usually February 2025.

Which upcoming date is cheapest to fly from Tokyo to El Nido Airport on?

After crunching the numbers on our flight calendar, we found that it is currently cheapest to fly from Tokyo to El Nido Airport on Friday, 5 September 2025.

Can I get a direct flight from Tokyo to El Nido Airport?

No airlines currently offer direct flights between Tokyo and El Nido Airport. Most routes have one or more stops.

How can I find the best flight deal to El Nido?

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 El Nido 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.

When is the best time to book flights to El Nido?

We crunched all the numbers in our flight calendar and it looks like the cheapest time to book a flight to El Nido is around 40 days in advance, so don’t leave your flight to the last minute.

Which is the cheapest airline to fly from Tokyo to El Nido with?

The cheapest airline that flies to El Nido is Zipair .

Flying from Tokyo to El Nido Airport (ENI): what you need to know

There are two main airports you can fly out of in Tokyo. Explore your options leaving from Haneda Airport (HND) or Narita International Airport (NRT) when searching for a flight from Tokyo to El Nido Airport (ENI).
El Nido Airport is located in El Nido. The city operates in the UTC+8 timezone and is 1 hour behind Tokyo.
For a smooth journey, turn up at the airport two hours ahead of international flights and an hour before domestic departures. This way, you can comfortably board your flight from Tokyo to ENI.
Flying over a peak time such as June? Major public holidays and other popular seasons can lead to longer lines and delays at check-in and security. Be extra cautious and get there up to four hours ahead of international flights and two hours before a domestic departure.

Airports in Tokyo

Haneda Airport (HND)

HND is around 16 kilometres from the centre of Tokyo. To work out how to get there, use Google Maps. This essential traveller tool will give you the fastest route and available public transport options.
Want a leisurely start to your travels? Stay near Haneda Airport. Whether you're catching an early flight from Tokyo to El Nido Airport or just don't want to be rushed, these hotels have you covered:

Narita International Airport (NRT)

Driving from central Tokyo to NRT typically takes 58 minutes, depending on traffic. It's roughly 64 kilometres from the city centre to the airport.
Want to treat yourself to an extra night away before boarding your flight from Tokyo to ENI? Relax in a hotel near Narita International Airport before your holiday officially starts. Stay at one of these accommodation options:

About El Nido Airport (ENI)

If you're arriving on a late flight from Tokyo to El Nido Airport, few things top the convenience of staying close to the terminal. Grab your bags from the carousel and then be showered and relaxing soon after at one of these options near ENI:

Getting from El Nido Airport (ENI) to central El Nido

From El Nido Airport, El Nido is approximately 2 kilometres away. It takes around 3 minutes to reach the centre driving.
If you're travelling by public transport, expect a journey of about 15 minutes.

How to find the cheapest flights from Tokyo to El Nido Airport (ENI)

For a one-way ticket from Tokyo to El Nido Airport, RM728 is the cheapest price. You can also book a return flight from just RM1,540. These are currently the lowest fares but could change depending on availability.
To score cheap tickets from Tokyo to ENI, book as early as possible. Airlines generally offer their most competitively priced fares when flights are first made available.
Getting cheap tickets from Tokyo to El Nido Airport is more likely if you're flexible with your trip dates. Check out the 'Whole month' tool to see the best prices throughout the month and bag a great deal.
Snapping up a cheap ticket from Tokyo to ENI is a piece of cake with Price Alerts. Simply set up one of these automatic alerts and we'll get in touch as soon as the price drops.
Use the filters to tailor your flights from Tokyo to El Nido Airport. Select your preferred arrival and departure times, airlines and number of stops. You can also sort your results by 'Cheapest' to get the best deals.

The best time to fly from Tokyo to El Nido Airport (ENI)

It's time to plan your travel dates for your flight from Tokyo to El Nido Airport. May is the busiest month to travel to El Nido. If you like a more relaxed atmosphere, go in February.
Before locking in your flight from Tokyo to ENI, think about the type of weather you enjoy. May is the warmest month in El Nido, with temperatures ranging from 26ºC to 30ºC.
Look for cheap flights from Tokyo to El Nido Airport in February if you like cooler conditions. Temperatures are at their lowest then, ranging between 25ºC and 29ºC on average.

More about El Nido

When it comes to looking for somewhere to lay your head, you'll find the top stays in El Nido right here. Check out these options as soon as you've locked in your flight from Tokyo to El Nido Airport:
One of the best ways to get a feel for El Nido is to visit its top sights. Essential stops include Big Lagoon, Secret Lagoon and Nacpan Beach.

Complete your El Nido trip with a car rental

Finding you a cheap flight from Tokyo to El Nido Airport isn't our only cool trick. Browse our car rentals in El Nido and explore on your own terms. We find deals from trusted car rental companies and put them all in one place. You can instantly compare offers and then book with no fees.