1979-1984 studied Nikžentaitis history at the University of Vilnius. 1984-1992 he was a research associate at the Lithuanian Institute of History. He was there his doctorate under Edvardas Gudavičius 1989. In 1992 he built together with Vlada Žulkus the research center for the history of western Lithuania and Prussia at the University of Klaipėda / Memel, which was re-organized with the Institute of History and Archaeology of the Baltic Sea Region in 2003. 1992-1993 Nikžentaitis was the first director of the center. He was appointed the first holder of the newly created Department of History at the University of Klaipeda in 1993. From 1998 to 2000 he worked as a fellow at the Herder Institute. In 1999 he habilitated with " The Lithuanian Society of the pre-Christian period (13th - 14th centuries) ". In 2000 he was appointed director of the Lithuanian Historical Institute. He served two terms until 2008. Nikžentaitis until 2004 was also at the Institute of History and Archaeology of the Baltic Sea region as the academic staff. By 2009 he was a professor of Lithuanian history at Vilnius Pedagogical University. 2009-2010 he worked as a fellow of the Alexander von Humboldt Foundation at the Humanities Center "History and Culture of East Central Europe " at the University of Leipzig. Since 2009 Nikžentaitis is the project coordinator and research associate at the Lithuanian Institute of History.
1999-2008 Nikžentaitis was a member of the scientific advisory board of the German Historical Institute in Warsaw. Since 2004 he has been Chairman of the Lithuanian historian Association, since 2005 Board member of the Lithuanian - German Forum, and since 2006 Chairman of the Lithuanian - Russian Historical Commission. He is also co-editor of the Journal of East-Central Europe research.
Nikžentaitis works focus on the recent history of East Central Europe. He operates mainly researches on the history of the enemy in the Baltic region, cultural memory, memory cultures in East Central Europe, the politics of history, identity change and symbolic appropriation of cities.
Writings (selection )
- Gediminas. Vyriausioji enciklopedijų redakcija, Vilnius 1989
- Pilėnų misle. Vyturys, Vilnius 1993, ISBN 5-7900-0449-0.
- As editor with Vlada Žulkus: Valletta miesto ir ir regiono archeologijos istorijos problemos. ( = Acta Universitatis Hictorica Klaipedensis. Vol. II ) Valletta Universiteto Leidykla, Klaipėda, 1994, ISBN 9986-505-00-3.
- Nuo Daumanto iki Gediminas. Ikikrikščioniškos Lietuvos visuomenės bruožai. ( = Acta Universitatis historica Klaipedensis. Vol. V). Valletta Universiteto Leidykla, Klaipeda 1996, ISBN 9986-505-21-6.
- As editor: Žemaitijos istorija. Regnum fondas, Vilnius 1997, ISBN 9986-494-35-4.
- Witold i Jagiello: Polacy i Litwini we wzajemnej stereotypy. Poznańskie tow. Przyjaciół Nauk, Poznan 2000, ISBN 83-7063 - 284- X (in Lithuanian:. Vytauto ir Jogailos įvaizdis Lietuvos ir Lenkijos visuomenėse Aidai, Vilnius 2002, ISBN 9955-445-54-8 )
- As editor with Stefan Schreiner and Darius Staliūnas: The Vanished World of Lithuanian Jews. Rodopi BV, Amsterdam - New York 2004, ISBN 90-420-0850-4.
- As editor: Nuo Basanavičiaus, Vytauto Didžiojo iki Molotovo ir Ribbentropo: atminties ir atminimo Kulturu transformacijos XX -XXI amžiuje. Lietuvos istorijos instituto Leidykla, Vilnius, 2011, ISBN 978-9955-847-37-3.