Aristeidis Agathoklis joined the Greek diplomatic service in 1974 serving in the central service of the Ministry of Foreign Affairs (NATO Directorate). From 1980 to 1985 he was the Secretary of the Permanent Representation of Greece in the European Economic Community (Brussels).

He served as Consul General in Hong Kong and Deputy Chief of Mission of the European Community Monitor Mission in former Yugoslavia. From 1994 to 1998 he was a member of the Greek delegation to the European Councils at Essen, Cannes, Madrid, Florence, Amsterdam, Luxembourg, Cardiff and Vienna. In 1999 he served in the European Affairs Office as Director in the diplomatic office of the then Minister of Foreign Affairs. From 2000 to 2003 he was the Permanent Representative of Greece to the EU.

From 2003 to 2005 he was the Ambassador of Greece in Spain and one year later, he served as a Special Adviser to the Minister of Foreign Affairs. He completed his career as Secretary General of the Ministry of Foreign Affairs in 2007-2008.