He had a distinguished career spanning over thirty years in the Danish Ministry of Foreign Affairs.

He served as deputy head of mission to the Danish Embassy in Pretoria, South Africa (1994 – 1998) and went on to serve as the Ministry's deputy head of Asian affairs (1998 – 2000) and head of Middle East and Latin American affairs (2000 – 2003).

During Denmark's 2002 presidency of the Council of the EU, Faaborg-Andersen co-authored the original Roadmap for the Middle East Peace Process (MEPP), eventually approved by the Quartet.

He concluded his career serving as the Danish ambassador to Portugal.

Faaborg-Andersen received his Master of International Affairs from Columbia University's School of International and Public Affairs (SIPA) in 1982 on a Fulbright scholarship and his Master in Political and Administrative Science (Cand.adm.pol) from the University of Copenhagen in 1984.