Between 1969 and 1973 Alfonsas Eidintas studied history at Vilnius Pedagogical University, going on to serve as chief lecturer, docent, head of the Universal History Department, and Deputy Dean at that institution. From 1986 to 1993 he was the Deputy Director for Research at the Lithuanian Academy of Sciences' Institute of History, receiving his habilitation in 1990.

Eidintas entered diplomatic service in 1993, serving as Lithuania's ambassador to the United States. He has also served as Lithuania's ambassador to Canada, Israel, Mexico, Cyprus, Ethiopia, South Africa, and Norway.

As of 2008, he had authored 16 books and 50 scientific articles about Lithuanian history and politics, and published a work of historic fiction, Ie?kok Maskvos sfinkso (In Search of the Moscow Sphinx).