Varghese's first diplomatic posting was at the Australian Embassy in
Vienna from 1980 to 1983. His second overseas posting was at the
Embassy of Australia, Washington, D.C. from 1986 to 1988. From 1989 to 1990, Varghese was a
speechwriter to
Foreign Minister Gareth Evans. Varghese's first Senior Executive Service appointment within the
Department of Foreign Affairs and Trade was as the Assistant Secretary of the Staffing Branch from 1991 to 1992. In 1994 he was posted to the Australian Embassy in
Tokyo. He was then the First Assistant Secretary of the Public Affairs Division from 1994 to 1996. As Head of the White Paper Secretariat from 1996 to 1997, Varghese led the drafting of Australia's first white paper on foreign and trade policy. He was appointed the First Assistant Secretary of the International Security Division in 1997 and then seconded to the
Department of the Prime Minister and Cabinet as First Assistant Secretary of the International Division from 1998 to 1999. Varghese was then appointed as Senior Adviser (International) to
Prime Minister John Howard from 2003 to 2004. an Australian government intelligence agency which reports directly to the
Prime Minister. From August 2009 to October 2012, Varghese was the
Australian High Commissioner to India, with concurrent accreditation to
Bhutan. Varghese was then appointed the Secretary of the
Department of Foreign Affairs and Trade in December 2012, serving until July 2016. When the
Abbott government took office in September 2013, Varghese had to oversee the integration of the Department of Foreign Affairs and Trade with
Australian Agency for International Development. It was announced on 24 November 2015 that he would be stepping down from the position in July 2016 to take on an appointment as chancellor of the University of Queensland. In 2016 Varghese joined the board of directors at
AMP Limited. His cousin Jacob was hired as a lawyer by the firm taking action against the AMP with regards to financial misconduct. == Honours ==