The Swiss presidency rotates every year between the seven members of the country's cross-party cabinet, with the role of the head of state largely symbolic.
Burkhalter, 53, is a member of the centre-right Liberal Radical Party and hails from the French-speaking region of Neuchatel.
The president is elected by the Swiss parliament, where Burkhalter received 183 out of 202 votes, underlining his strong support across the country's political divides.
Maurer, a member of the right-wing populist Swiss People's Party, received 148 votes when he was elected in December 2012.
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Burkhalter's party colleague Economy Minister Johann Schneider-Ammann received 10 votes.
Burkhalter was elected to the cabinet -- or Federal Council -- in 2009 and started out as interior minister before taking the foreign affairs portfolio in January 2012.
As foreign minister, he set a goal of boosting Switzerland's ties with the 28-nation European Union, of which it is not a member.