The Iraqi transport ministry heralded the flight as a major breakthrough.
"Transport Minister Amr Abduljabbar Ismail was on board the plane, which made a stop-off in the Greek capital" where he held talks with Greek leaders on developing bilateral relations in transport, the Iraqi transport ministry said in a statement.
Friday's flight then continued to the Swedish capital, Stockholm.
Iraqi Airways planes have been grounded since an international embargo was imposed
after Iraq invaded Kuwait in August 1990.
Following the US-led invasion in 2003, the company resumed air services to Arab countries, Iran and Turkey, among other destinations.
The transport ministry said Iraqi Airways plans to add scheduled flights to Bahrain, Germany, India and Qatar.
The ministry and Air France-KLM signed an outline agreement on December 30th 2008 for the operation of commercial flights to Europe and for the renovation of Baghdad airport.
Among the clauses, Air France-KLM undertook to help Iraqi Airways set up international flights, especially European services.
The agreement also covers the renovation of Baghdad airport's terminal three to international standards and the construction of new airports in Iraq with funding
from French businesses.
In January, Swedish charter company Nordic Leisure carried out the first passenger flight between Iraq and Europe since 1991, but the company lost its operating licence later the same month.
Sweden is among the European countries that have taken in the largest numbers of Iraqis fleeing the violence in the home country.