From 1988 to 2008, Aghabekian was a professor at Al-Quds University in Jerusalem. She was initially an associate professor before holding a number of administrative positions, including dean of the faculty of health professions from 1995 to 1998 and dean of graduate studies from 1998 to 2000.[1][3]
She has held key positions in a number of cultural and social projects as well. She served as the coordinator of the human resources development unit of the Palestine Medical Council, director of the institutional building project at the office of the Palestinian president, executive director of the 2009 rendition of the Arab Capital of Culture programme, and commissioner-general of the Independent Commission for Human Rights (2016–2018).[3][4] Additionally, she is a board member of the Diyar Consortium, a Palestinian organization focusing on cultural and educational development.[2]
An Armenian Christian, Aghabekian is a founding member of the presidential commission for the restoration of the Church of the Nativity, as well as the presidential commission for church affairs.[1][3] She is an advocate of Christian and women's rights in Palestine.[3]
On 23 June 2025, President Abbas approved the reshuffle of the government of Mohamed Mustafa, and Varsen Aghabekian became minister of foreign affairs and expatriate affairs in place of Mohamed Mustafa. On 15 July 2025, the EU's top diplomat Kaja Kallas and the foreign ministers of the EU member states agreed not to take any action against Israel over alleged Israeli war crimes in the Gaza war and settler violence in the West Bank.[10] The proposed sanctions against Israel included suspending the EU-Israel Association Agreement, suspending visa-free travel, or blocking imports from Israeli settlements.[11] Aghabekian criticised the decision, saying: "It's shocking and disappointing, because everything is crystal clear.... The whole world has been seeing what is happening in Gaza. The killing, the atrocities, the war crimes."[11]
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