Federer, 33, came ahead of second place Dario Cologna, the cross-country ski champion who was voted top sportsman last year.
The Basel native won five ATP tournaments this year — although no grand slams — in addition to helping Switzerland’s men’s tennis team to win this year’s Davis Cup.
Television viewers elected the squad top Swiss sports team of the year, although one of the members, Stan Wawinka was unable to attend the award ceremony because of illness.
Wawrinka came third in the vote for best sportsman in the country after winning the Australian Open and also participating in the Davis Cup.
Federer earlier won the same sportsman of the year award in 2003, 2004, 2006, 2007 and 2012.
Gisin, 29, was honoured for earning a gold medal at the Sochi Olympics earlier this year when she tied for first place in the skiing downhill competition with Slovenian Tina Maze.
The native of Engleberg in the canton of Obwalden has won three World Cup races in her career.
Among the other awards, runner Kariem Hussein, 25, was named “newcomer of the year” for having won a gold medal in the 400-metre hurdles competition at the European athletic championships earlier this year.