Hoxhaj served as a professor at the University of Prishtina. He worked at WUS Austria and founded Kosovar Research and Documentation Institute. In March 2004 he joined the Democratic Party of Kosovo. He was Minister of Education, Science and Technology of the Republic of Kosovo. He served twice as a Foreign Minister, once from 2011 to 2014, under the mandate of the government led by Hashim Thaci, and the second time he was named as a Foreign Minister started in June 2016, under Prime Minister Isa Mustafa.