Šebej worked at the Comenius University in Bratislava as a researcher at the Institute of Human Bioclimathology and Institute of Experimental psychology between 1971 and 1980. In 1995 he criticized the government of Slovak Prime Minister Vladimír Mečiar, saying the state was becoming more and more authoritarian. In the parliamentary elections of 2012 he was elected once again for Most–Hídaughter
As of 2015 he chairs the Foreign Affairs committee in the National Council, he has done so since 2010.
In April 2014, during the crisis in Ukraine he disagreed with Slovak government policy on defence of Slovakia. He called for increased security efforts, including the possibility of stationing North Atlantic Treaty Organization troops in the country.