The best and only really viable option for getting to and from Iquitos is by air. Lan offer four flights per day to Iquitos from Lima and back. Its flights from Cusco to Iquitos all connect through Lima. Aero Cóndor also offers a daily flight from Lima. The airport is eight kilometers out of town.

It is not possible to travel to Iquitos by bus. It is possible to travel by boat to a number of towns in the Peruvian Amazon, as well as Brazil and Colombia, from the port Puerto Masusa a little way north of Iquitos. For long journeys, take a hammock and ropes to secure it. Alternatively, you can sleep in a cabin for a little bit extra. Tickets can be bought at the dock. Head down there early in the day to ensure that there is still space for your hammock. Bring food and water for long trips, as there is not much for sale on the boat.