Heinen-Kljajic was elected to the Lower Saxon Landtag in 2003 state elections, and has been re-elected in 2008 and 2013. On February 19, 2013, she was sworn in as State Minister for Science and Culture in the government of Minister-President Stephan Weil. As one of her state's representatives at the Bundesrat, she served on the Committee on Cultural Affairs.
When the Green Party had to leave the coalition government following 2017 state elections, Heinen-Kljajic was succeeded by Björn Thümler.