How to get from El Nido to Manila

Why visit Manila?

Manila is the capital of the Philippines — an old city often disregarded by travellers who use it only as a gateway to the country’s more visually appealing islands. But if you have an extra day in your itinerary, we think Manila’s colourful history is a great way to kick off your trip.

Explore the walled city of Intramuros, Fort Santiago, Manila Cathedral and San Agustin Church — all of which were first built in the late 1500s. Art and anthropology also attract many locals to Manila. You will find here the National Museum, a complex of three museum buildings that tell the story of the Filipinos.

There are 5 ways to travel the 623 kilometres (387 miles) from El Nido to Manila. You can choose between the direct flight, direct ferry, minivan + flight via Puerto Princesa, minivan + flight via San Vicente* and indirect ferry via Coron. The journey takes 2 hours 20 minutes to 1 day 6 hours and the quickest way is by direct flight. If you're on a budget, the cheapest option is by direct ferry with tickets starting at 1,840 PHP ($31.50).

The most popular option to travel from El Nido to Manila is a combination of a 5 to 5.5-hour minivan ride to Puerto Princesa and a 1.5-hour flight to Manila.

Even though there are direct flights from El Nido to Manila, more airlines operate from Puerto Princesa to Manila and fares are cheaper for this route. In fact, combined fares for this indirect flight option are less than half of the direct flight fare from El Nido to Manila.

From El Nido Transport Terminal, there are multiple minivans bound for Puerto Princesa. Fortwally, Eulen Joy Express, and Island View Travel vans head straight to Puerto Princesa Airport, so you won’t need any additional rides.

The van ride can take 5h with fares from 700 PHP ($12).

We highly suggest booking online in advance via BookAway if you have already booked your flight from Puerto Princesa to Manila. This way, you can plan your trip from El Nido to Puerto Princesa Airport accordingly without missing your flight.

The second leg of your trip is a flight from Puerto Princesa to Manila, which takes around 1h 30m — same as flying direct from El Nido. AirAsia, Cebu Pacific, and Philippine Airlines all fly this route, with ticket prices starting at 1,350 PHP ($23).

Airfares tend to get more expensive if you book shortly before the flight — especially during busy seasons — so it’s a good idea to book early.

TIP: Cebu Pacific and AirAsia offer many promotions annually. Keep an eye out for these promotions to book a cheaper flight for this route!

Flights from Puerto Princesa to Manila land at Ninoy Aquino International Airport (NAIA) in Pasay City. Manila Airport has 4 separate terminals with different entry points. AirAsia and Philippine Airlines flights land at NAIA Terminal 2, while Cebu Pacific lands at Terminal 3. These terminals are about 10 minutes apart.

The easiest way to get from Manila Airport to anywhere in Metro Manila is by Grab car. Rates start from 230 PHP ($3.90) from Terminal 3 and 370 PHP ($6.40) from Terminal 2, depending on where you’re heading in the city. Taxis are also available at the airport, just make sure you travel with an accredited taxi!

If you want to pre-book your transfer, Klook offers private rides with prices from 1,170 PHP ($20) for a 4-seater.

Alternatively, UBE Express operates point-to-point buses from several destinations across Metro Manila to Ninoy Aquino International Airport. Here are the ticket prices:

• • 150 PHP ($2.60) – to Pasay, Parañaque and Robinsons Manila
  • 200 PHP ($3.40) – to Araneta City and Alabang

Check out our guide for Manila Airport for more details.

The direct flight is the fastest option from El Nido to Manila, but it is also the most expensive. It’s ideal if you’re short on time and don’t mind spending a bit more.

AirSWIFT and Cebu Pacific offer direct flights on this route. Including airport transfers, the total travel time comes to around 2 hours 20 minutes to 2 hours 50 minutes.

TIP: If you decide to travel by plane, please consider including a carbon compensation fee to reduce your impact on the environment.

Flights depart from El Nido Airport, which is only 5 km away from the town centre. A tricycle ride from your hotel to the airport costs 300 PHP ($5.20) for 2 passengers with luggage.

You can also check with your hotel if they offer transport to the airport.

AirSWIFT and Cebu Pacific run several direct flights from El Nido to Manila every day. The earliest flight takes off at 07:40, and the last one leaves around 20:15. The journey takes about 1h 30m

One-way tickets start at 6,900 PHP ($120), but prices tend to climb as your travel date gets closer. If you want to lock in the best deal, it’s a good idea to book early.

The direct flight from El Nido to Manila lands at Ninoy Aquino International Airport (NAIA) in Pasay City. AirSWIFT flights arrive at Terminal 2, while Cebu Pacific (5J) lands at Terminal 3.

The easiest way to get around after landing at Manila Airport is by Grab car. Just book through the app, and you’re good to go. Fares start at 230 PHP ($3.90) from Terminal 3 and 370 PHP ($6.40) from Terminal 2, depending on your destination.

Taxis are also available, but make sure to take an accredited taxi to avoid any issues.

If you want everything sorted before you arrive, you can pre-book a private transfer with Klook. Prices start at 1,170 PHP ($20) for a 4-seater car.

Check out our guide for Manila Airport for more details.

Travelling by ferry from El Nido to Manila is an option, if you’re not in a hurry. You can take an indirect ferry from El Nido to Manila that takes around 16 hours 30 minutes.

You’ll first need to take a fast ferry from El Nido to Coron Port, and then another ferry from Coron to Manila North Harbour Pier 4. This is a good option if you want to explore the beautiful island of Coron.

There are four fast ferry companies operating between El Nido and Coron.

Phimal offers the cheapest ferry tickets, with prices starting at 2,600 PHP ($44.50). But it only runs on select days — Tuesday, Thursday, and Saturday mornings.

Other operators like Montenegro Shipping Lines, Jomalia Shipping, and Atienza Interisland Ferries are available daily. Their tickets are pricier, though, ranging from 2,690 PHP ($46) to 3,060 PHP ($53).

Travel time is about 3h 30m - 3h 40m.

For more information, you can visit our page on El Nido to Coron.

2Go Travel is the main operator for ferries from Coron to Manila. It is one of the most famous ferry companies in the Philippines, so it is often the first choice for sea travel. There’s a catch, though, the 2Go ferry from Coron to Manila operates only on Sundays.

Travel time takes 13h to Manila North Harbour with fares starting from 3,110 PHP ($53). But this price still depends on how early you book and on the ticket class you buy. You’ve also got the option to book directly on their official website.

If you’re after a direct ferry trip from El Nido to Manila, Atienza Interisland Ferries is your only option.

The company has two departures a week, typically on Tuesdays and Fridays. Schedules can change, so we recommend checking their Facebook page for the latest updates.

Economy class tickets cost 1,840 PHP ($31.50), while an airconditioned tourist class ticket costs 2,060 PHP ($35.50).

Departure and arrival ports

All ferries leave from El Nido Ferry Terminal and arrive at Baseco Port Area in Tondo. This pier is accessible to other cities in Metro Manila via taxi or Grab, with fares starting at about 250 PHP ($4.30).

El Nido

Economy

Baseco Port

08:00

30h

14:00

11:00

30h

17:00

17:00

30h

23:00

Atienza Interisland Ferries

From 1,840 PHP ($31.50)

Compare prices

• 24/7 customer support

1,840 PHP ($31.50)

11:00

30h

17:00

17:00

30h

23:00

Check on BookAway

• 24/7 customer support

2,600 PHP ($44.50)

08:00

30h

14:00

Check on BookAway

El Nido

Premium

Baseco Port

08:00

30h

14:00

11:00

30h

17:00

17:00

30h

23:00

Atienza Interisland Ferries

2,060 PHP ($35.50)

Compare prices

• 24/7 customer support

2,060 PHP ($35.50)

11:00

30h

17:00

17:00

30h

23:00

Check on BookAway

• 24/7 customer support

2,810 PHP ($48.50)

08:00

30h

14:00

Check on BookAway

The last time we checked (June 2025), there were no available flights from San Vicente to Manila. Please click the link provided to see if anything has changed.

Aside from El Nido and Puerto Princesa, San Vicente has a small airport where you can take a flight to Manila. This town is located 2 to 3 hours away from El Nido, so travel time is shorter compared to taking a flight via Puerto Princesa.

San Vicente is a budding tourist destination in Palawan. You’ll find here the longest white sand beach in the Philippines, which makes for a good side trip opportunity before heading to Manila.

This option includes a 2-hour minivan ride from El Nido to San Vicente and a 1-hour-45-minute flight with Sunlight Air from San Vicente to Manila.

Since San Vicente is a small town with only two flights a week at its airport, public transportation is not regularly available.

For this reason, Sunlight Air, the sole airline operating between San Vicente and Manila, offers minivan transfers for its passengers. Tickets cost 785 PHP ($13.50) one way, and you can book your seat through their Facebook page.

The minivan will pick you up from El Nido Terminal and drop you off at San Vicente Airport in time for your flight to Manila.

We suggest booking your seat with Sunlight Air, especially since the flight is early in the morning. If by public transportation, you will need to take a bus or a minivan to Roxas town or junction and then ride an e-tricycle (electric tuk-tuk) to San Vicente Airport.

Sunlight Air offers flights between San Vicente and Manila twice a week. The flight departs San Vicente at 07:00 on Sundays and Thursdays.

Airfares start from 3,000 PHP ($52), but you can score cheaper tickets during seat sales.

It takes around 1h 45m from San Vicente to Manila by flight.