The only scheduled domestic service within Guatemala is between Guatemala City and Flores, although ongoing improvements to local infrastructure at many smaller airports may mean a small network of local flights may soon be up and running. Some of the flights to and from Flores operate using smaller aircraft, though the largest bird on this route nowadays is the ATR-42. Airfares for this domestic service have recently skyrocketed and are surprisingly expensive, particularly when taking into account the short distance involved in flying within Guatemala.

All of the domestic carriers flying out of Guatemala City operate from their private hangars, located on the east side of the runway, opposite the main terminal building. The only airline operating its domestic service from the main terminal at La Aurora airport is TACA.

New domestic airports with passenger terminals are either complete or nearing completion in Huehuetenango, Quetzaltenango, Puerto San José, Coatepeque, and San Marcos. Plans call for terminals at the Pacific Coast leisure destination of Retalhuleu and the existing paved runway at Puerto Barrios. Cobán has a functional airstrip, though there is no scheduled service.

Flights from Guatemala City to the above destinations may become a reality once the terminals are complete and investors make inroads into a market with certain potential. During the late 1990s, TACA subsidiary Inter operated domestic air service between Guatemala City and Cobán, Quetzaltenango, Huehuetenango, and Puerto Barrios.