Papandreou was sworn in on Tuesday after his election victory over Costas Karamanlis. He will also be responsible for foreign affairs in his cabinet.
Papandreou, who will be accompanied by Deputy Foreign Minister Dimitris Drucas, will arrive in Istanbul early Friday and he will leave in the evening the same day, officials said.
Earlier reports had said Papandreou would make his first overseas trip to Greek Cypriot administration on a formal visit. His visit to Turkey will not be a formal one, diplomats said.