"This is the first step for Iraqi Airways. We hope to expand our services to Dubai within weeks," an airline official said.
Airline official Fathi Nassar said the plane left the Jordanian capital without any passengers because the resumption of flights was announced too late for tickets to be sold.
The airline said it will launch scheduled flights to neighbouring Arab countries Syria and Jordan twice a week.
More international flights could help boost Iraq's reconstruction by providing more travel alternatives for businessmen and investors keen to avoid highways plagued by bandits and gunmen.
But with security in the country deteriorating, and a wave of kidnappings of foreigners on the upsurge, many foreigners still choose not to come. Until now there have only been a few daily commercial flights in and out of Baghdad, almost all to Amman.
Iraqi Airways says its offices have already sold dozens of tickets, but at prices the majority cannot afford. A return ticket to Damascus would cost $600, and a return to Amman $750. The same trip by road costs about $40.
After successfully performing a test flight from neighbouring Jordan in August, Iraqi Airways was initially denied regular airspace permission to fly over Iraqi territory, with doubts over licensing validity stalling the process.
But approval has now been granted, meaning Iraqi Airways can compete with Royal Jordanian which already has scheduled flights in and out of Iraq.
Foreign troops still guard the
airport that the airline will use
Despite the airline's optimism, it faces many hurdles. Many of its financial assets have been frozen since last year and only one of its 16-plane fleet is currently operable.
Iraqi Airways was formed in 1946. After Iraq's invasion of Kuwait, UN sanctions imposed an economic embargo in 1991 that left the airline in ruins.
Fifteen of its planes were flown out of the country, where they were left to rust. The airline says the planes are "non-functioning" and says it will send out repair teams.
Hit by sanctions
Domestic flights were barred by the no-fly zones in northern and southern Iraq set up by the United States and Britain after the first Gulf war.
The sanctions forced the airline to turn to maintenance work on other international planes to avoid falling into bankruptcy.
"We were not allowed to fly. We turned our offices into business centres and we turned to contractual work in Libya, Jordan and Sudan," said Isac Esho, the airline's deputy director general.
While many airlines have been reluctant to use Baghdad International Airport - fearing a disaster is inevitable in a country plagued by violence - Iraqi Airways says an attack on its planes is unlikely.
"We're not scared. Our aircraft will take the same security risk as all the others, probably much less," Esho said.