Three flights between the Iranian and Greek capitals will be operated per week, the commercial director of Aegean Airlines said.
He added that the flights are scheduled to be carried out by Airbus A320s on Sundays, Tuesdays, and Thursdays.
In a meeting between the Iranian and Greek foreign ministers in Athens earlier in May, the two sides had discussed the establishment of a direct flight route between Tehran and Athens.
The two sides also stressed the need for the expansion of economic relations between the two countries by stimulating bilateral trade in diverse fields.
Iran and Greece, known as popular tourist destinations for their rich histories, seem more willing to strengthen ties after Iranian President Hassan Rouhani took office in August 2013.
In April, when submitting his credentials to President Rouhani, Greece's new ambassador to Iran George Aifantis hailed Iran as an independent and influential country in the Middle East and Asia, saying Athens wants to be Tehran's "strategic friend" and partner.