Burkhalter is a member of FDP.The Liberals. He was elected as a member of the Swiss Federal Council on 16 September 2009. He succeeded Pascal Couchepin on 1 November 2009 when he became head of the Federal Department of Home Affairs (the Swiss interior minister). From 1 January 2012 to 31 October 2017, he served as head of the Department of Foreign Affairs. In 2014 he was President of the Swiss Confederation. He served as Chairman-in-Office of the Organization for Security and Co-operation in Europe (OSCE) in 2014. He left the Federal Council on 31 October 2017.
A native of the Canton of Neuchâtel, Burkhalter served in the Parliament of the Canton of Neuchâtel from 1990 to 2001. From 1991 to 2005, he was a member of Neuchâtel's city government (Conseil communal), and was the mayor of the city several times (1994/1995, 1998/1998, 2001/2002). From 2003 to 2007, he was a member of the Swiss National Council.
On 11 November 2007, Burkhalter was elected to the Council of States, along with Social Democratic Party (SP) candidate, Gisèle Ory, who was re-elected for a second term. During the election campaign, he was backed by the Liberal Party (PLS) and the SVP/UDC.
On 1 January 2014 Burkhalter assumed the office as President of the Swiss Confederation. As President of the Confederation, he presides over meetings of the Federal Council and carries out representative functions that would normally be handled by a head of state in other democracies (though in Switzerland, the Federal Council as a whole is regarded as the head of state). He is also the highest-ranking official in the Swiss order of precedence, and has the power to act on behalf of the whole Council in emergency situations. However, in most cases, the President is merely primus inter pares, with no powers over and above his six colleagues.
Burkhalter has a degree in Economics, is married to a native Austrian, and is the father of three children.
On 14 June 2017 Burkhalter published a letter in which he announced that he will be resigning as Federal Councillor on 31 October 2017. He was succeeded by Ignazio Cassis. In April 2018, Burkhalter stated he disagreed with his colleges on arms exports to war zones and equal pay for men and women, issues he described as "fundamental values."