The trip comes in two stages: an international flight into mainland Ecuador, then a domestic flight out to the archipelago from Quito (UIO) or Guayaquil (GYE) — flights from Quito normally make a technical stop in Guayaquil on the way. Count on around two hours in the air from Guayaquil, and around two and a half from Quito with the stop. The route is flown by Avianca Ecuador and LATAM Ecuador; schedules and fares change with the season, so check them directly with the carriers when you plan.
You will not find a flight timetable on this page, because there is no honest way to publish one: departure times and fares shift through the year. What never shifts is the mechanism — and the money collected at the door. Two payments stand between the plane and the islands, both per person, and neither is included in the price of a land-based tour.
