Some 100 passengers were on board the aircraft on Thursday, including 20 journalists from various Iraqi media organisations, led by Ahmed Abdul Wahab, a media adviser at the Iraqi transportation ministry.
Egyptian civil aviation officials and Iraqi embassy staff, including charge d'affaires Saad Orabi, welcomed the party at the airport.
"The arrival of this plane is proof of Iraq's return into the international community and the beginning of a new era," Orabi said.
Iraqi Airways will offer bi-weekly flights to Cairo on Mondays and Thursdays.
Commercial flights to and from Iraq were suspended as a result of UN sanctions slapped on that country after its forces invaded neighbouring Kuwait in 1990.