By plane
There are daily local flights from and to Quito, Guayaquil and neighboring countries as well. Currently TAME (http://www.tame.com.ec/ta...) and AeroGal both offer daily service to Cuenca. AirCuenca offers service every day except Sunday.
A taxi from the airport to the center should run about $2.
By Bus/Car
Cuenca lies on the Pan-American highway. Buses offer connections to many cities in Ecuador.
Loja for connections to Vilcabamba 4.5-7 h, $7.5. Be warned that the Viajeros buses to Loja do not have a working bathroom and they can take up to 7 hours we were told at the office that it would take 4 hours and that it would only make one stop, but we stopped more than 50 times and ended up so full the bus could hardly struggle uphill. This was with Viajeros "International".
San Luis buses run from Cuenca to Loja using the national park route and take 4.5 hours, $8. Departures at 7.45am, 11am, 4pm, 7.30pm and 12 midnight. There is a working toilet.
Alausi. 4 hours Transportes AlausiRiobamba. 6 hours Patria
Piura, Peru: There is a new service to Piura leaving at 19:30, 21:00 and 23:00. This is a partnership between two companies, Pullman Sucre and CIFA International. It is necessary to change bus at either Machala or Huaquillas. The 19:30 and 23:00 services connect to a special sleeper seat service. The price is 12$-15$ depending on the class of service. It is a good idea to purchase your ticket a day in advance as it is not unusual for them to book out.
Tumbes, Peru: As above, plus additional departures at 13:15 and 15:00. $7 from the border.
There is a $0.10 departure fee for leaving from the bus terminal.