The flight time depends you departing city, this Flights to the Galapagos leave from Quito making a stop in Guayaquil so you don’t have to necessarily board in Quito to get from Quito to Guayaquil takes about thirty minutes and about one and a half hours from Guayaquil to the Galapagos Islands. All flights leave from 7am to 11am in the morning and return between 1pm and 5pm.