Guide to Combining the Galapagos Islands and Machu Picchu



Here are the two main itinerary options for combining your trips; please note the transportation times and necessary stops along the way.

Day 1:   Arrive in Quito (or Guayaquil).  Overnight in the city.
Day 2 – 9:  Galapagos Cruise
Day 9:  Fly back to mainland Ecuador in the afternoon.  Overnight in Quito or Guayaquil.
Day 10:  Fly from Quito (or Guayaquil) to Lima in the morning.  Connect with your Lima to Cusco flight.  Rest Day in Cusco.  Overnight in Cusco
Day 11:  Sacred Valley Tour.  Overnight in Cusco.
Day 12:  Train from Cusco to Machu Picchu.
Day 13: Free morning at Machu Picchu.  Afternoon train back to Cusco.
Day 14:  Fly Cusco to Lima to home.


Day 1:   Arrive in Quito (or Guayaquil).  Overnight in the city.
Day 2 – 9:  Galapagos Cruise
Day 9:  Fly back to mainland Ecuador in the afternoon.  Overnight in Quito or Guayaquil.
Day 10:  Fly from Quito (or Guayaquil) to Lima.  Connect with your Lima to Cusco flight.  Overnight in Cusco
Day 11:  Rest Day in Cusco
Day 12 – 15: Hike the Classic Inca Trail to Machu Picchu
Day 15:  Last day of Inca Trail.  Tour of Machu Picchu.  Afternoon train to Cusco.
Day 16:  Fly Cusco to Lima to home.


We can arrange all the internal flights for you, however, we cannot usually provide the flights between Ecuador and Peru. Typically, the easiest and cheapest international flights for your trip will be the “open jaw” itinerary. This is where you fly into one city, but fly back home from a different city.

For instance, with the “Galapagos and Machu Picchu” itinerary above, you would book the following flights through your international carrier:

  Day 1: Home – Quito
  Day 10: Quito – Lima
  Day 14: Lima – Home

We automatically book your flights between mainland Ecuador and the Galapagos (this is required by all local Galapagos operators) and the rate will be added to your total Galapagos trip price. That price as of 2012 is approximately $580 per person in the high season and very rarely fluctuates.* For the flights between Lima and Cusco you have the choice of either booking it yourself or through Detour (rates are approximately $350 roundtrip, this rate fluctuates quite a bit).

*Ecuador’s President, Rafael Correa, ended all government fuel subsidies for local airlines. As of 2012 all flights to/from the Galapagos reflect the increase in cost. For those whose flights have already been booked/issued you will be expected to pay a fuel surcharge of approximately $70 (one-way) at the airport upon checking-in.


The city of Cusco is the major hub for visitors going to Machu Picchu.  It is a beautiful and fascinating city with lots of Incan history.  It is essential to spend a bit of time in Cusco getting used to the altitude; plus, the trains to Machu Picchu leave early in the morning, which means you cannot fly into Cusco and take off for the ruins in the same day.  Likewise, you need to stay the night in Cusco when you return from Machu Picchu.  This is because there are no evening or night flights between Cusco and Lima (the mountain weather makes it too dangerous).  So you have to fly in the morning between the two cities.


No. Think of this as flying from Yellowstone National Park to the bottom of the Grand Canyon; you need to get to an airport and use other transportation to get to the actual destination.  From the Galapagos, you have to fly to Quito (or Guayaquil) and then fly to Lima.  At that point, you then have to fly to Cusco and overnight in Cusco (the city nearest to Machu Picchu), prior to visiting the ruins.  From Cusco, you can either hike to Machu Picchu (via the Inca Trail) or take the train.


Ideally, you should sleep at high altitude 2 nights prior to your trek, while resting during the day.  However, 24 hours of acclimatization is adequate prior to starting the Inca Trail trek.  If you’re doing a more challenging or higher trek (such as the Ausangate or Choquequirao treks), you should go with the 2 nights acclimatizing beforehand or 36 hours total at altitude.  Altitude sickness can be a very serious, even deadly, problem so you should do all you can to properly acclimatize and avoid getting sick.


It is possible to fly to Lima the night after your Galapagos cruise ends, it’s just more of a hassle.  First of all, you cannot fly from Lima to Cusco at night.  The weather over the Andes makes this too dangerous.  Therefore, you need to overnight in either Guayaquil, Lima or Quito after your Galapagos cruise.  There are only a couple flights each evening between Guayaquil/Quito and Lima; so your flight options are limited.  Additionally, Lima hotels are all about 45 minutes from the airport, which adds on a lot of transportation time.  Quito is a much prettier and tourist-friendly city, so people typically enjoy their final night there.  It’s also much nicer than Guayaquil, so It doesn’t add-on any extra time to your itinerary to overnight in Quito instead of Lima, so we usually recommend people just connect through Lima in the morning, en route to Cusco.


It’s very worthwhile to spend one extra day in Quito prior to your Galapagos trip, both for a time cushion (what if your international flight is delayed?) and because the city is truly fascinating – the Old Town is a UNESCO World Heritage Site.

If you’re doing the Inca Trail Trek, you ought to consider doing the 5-day trek over the 4-day trek. That way, you’ll have an extra morning to check out Machu Picchu and the pace of the trek is much more reasonable.

If you’re doing a cultural tour in Peru, an extra day in the Sacred Valley or in the Cusco area is highly recommended. We think the Qosqo Llacta itinerary is ideal and it comes highly recommended from other travelers.  If you want to be active, you can do one-day of horseback riding, hiking, whitewater rafting or mountain biking in the area.


The bare minimum is four days: one day to fly to Cusco, one day to acclimatize, one day to see Machu Picchu and one day to fly out of Cusco (to Lima and then onwards).  This is not a highly recommended way to visit Peru and you’ll be missing some of the best parts of the area (such as touring Cusco, visiting the stunning Sacred Valley and seeing Machu Picchu an extra day).  However, if you’re committed to seeing Machu Picchu in the least amount of time, a four-day extension is possible.


Below is the absolute fastest version of this trip (though a 4-day Galapagos trip is not the recommended way to see the Islands — a 5-day cruise is much better)

Day 1: Fly Home – Quito. Overnight in Quito.
Day 2 – 5: Galapagos 4-day Trip
Day 5: Overnight in Quito
Day 6: Fly Quito – Lima – Cusco
Day 7: Tour of the Sacred Valley
Day 8: Machu Picchu Tour
Day 9: Fly Cusco – Lima – Home
Galapagos cruises are typically 4, 5, 6 or 8 days in length, but a land-based Galapagos trip can be any number of days.  If you want to see the Galapagos in 6 days, then visit Peru for 5, that’s a great tour.  See some of our other itinerary suggestions below for more ideas.


While you’re in South America, there’s a lot to see besides the Galapagos Islands and Machu Picchu.  We suggest visiting the Amazon rainforest; hiking through the Andes; or exploring the historic colonial cities in Ecuador and Peru.  These are all surprisingly easy extensions to your Galapagos vacation and well worth the extra time.

Here are some suggestions on other destinations to visit, depending on how many extra days you have.

1 Day Extra:
    Quito city tour with visit to Mitad del Mundo, Equatorial line (Ecuador)
    Hike, bike or horseback ride in Cotopaxi National Park (EC)
    Raft on the Urubamba River (Peru)

2 Days:
    Raft trip outside Quito (EC)
    Stay in a Hacienda near Otovalo Market (EC)
    Two-day hike to Inca ruins with camping (PR)
    Kayaking and horseback riding in the Andes (EC)
3 Days:
    Quick visit to a rainforest lodge, like Posadas Amazonas (PR)
    Three days of mountain biking in the Sacred Valley and Lares Valley (PR)
    Visit Cuenca and Ingapirca (nearby Guayaquil) (EC)

4 Days:
    Visit to an Ecuadorian jungle lodge, like the Napo Wildlife Center (EC)
    Explore the Andean Countryside on the “Due South” trip (EC)
    Extend your Galapagos stay by staying on the most beautiful island, Isabela (EC)
    Hike through the stunning Lares Valley (PR)

5 Days:
    Stay at a lodge deep in the rainforest, like the Huaorani Ecolodge (EC) or the Tambopata Research Center (PR)
    Hike to Machu Picchu’s sister city, the Choquequirao ruins (PR)
    Visit the Colca Canyon and Arequipa, the white city (PR)
    Tour the impressive Kuelap ruins and northern Peru’s countryside (PR)

6 Days:
    Travel overland from the Andes to very impressive Manu National Park (PR)
    Explore mountains, cloudforests and coast by bike, kayak, and foot (EC)

7 Days:
    Hike the Ausangate Circuit, one of the most beautiful in Peru (PR)
    Do a two week, instead of one-week, Galapagos cruise to really see the Islands (EC)
    Trek in luxury to Machu Picchu with a Lodge-to-Lodge trip (PR)

11 Days:
    Multi-Activity in Peru– a very adventurous way to see the highlights (PR)

13 Days:
    For a rewarding and truly remote adventure, do the Choquequirao to Machu Picchu Trek (PR)
    Bike from Lake Titicaca to Cusco over the rugged altiplano (PR)
    Whitewater rafting from Lake Titicaca to the Amazon rainforest (TR)

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