The airline was established on 1929 as Aerovías de Guatemala, and was founded by Alfredo Denby Chattfield. In 1945, the airline was nationalized during the government of Juan José Arevalo and stablished as Empresa Guatemalteca de Aviación S. A., which was shortened to Aviateca. One of the original founders was Alfredo Castaneda Duarte who also served as a pilot. Aviateca started operations in March 1946 and early aircraft operated by the carrier included the Douglas DC-3.

In 1961, service to Miami was originated with four-engined Douglas DC-6 airliners. Convair 340/440 twin-engined medium airliners were also acquired to replace some of the DC-3s on short-haul routes in Latin America. Aviateca was a customer for the BAC One-Eleven medium twin jet in 1970.

It also temporarily leased a Fokker F28 Fellowship, a Boeing 720 and a Douglas DC-8 in the 1970s. Aviateca later acquired two Boeing 727s, which operated for the airline in the 1980s. From 1989 on Aviateca's fleet consisted of several Boeing 737-200 and Boeing 737-300 jetliners. A full cargo Boeing 737-300 was also operated for a few months.

Aviateca was under government ownership and remained so until 1989 when it joined the TACA-organised Airline Alliance of Central America and was privatised. It was fully integrated into TACA, which later merged with Avianca.

The aircraft were referred to by locals as "las papayas voladoras" (the flying papayas) due to the paint scheme used during the 1970s, in which the underbelly was painted a reddish orange. Later Aviateca switched to blue. From 2006 to 2007 Aviateca had a TACA Airbus A319 aircraft with the TACA-style Aviateca logo on the engines.

TACA Regional (formerly Inter and operating under Aviateca's IATA code) has two ATR 42-300s.

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