The Swiss Olympic Committee says the 27-year-old Wawrinka "fulfills the requirements of this prestigious task."
Wawrinka and Federer will defend the men's doubles title they won in Beijing four years ago, one of two events in which Switzerland took gold.
Wawrinka says "I'm proud of carrying the Swiss flag. It reminds me of the great moment where I received the medal in Beijing with Roger Federer."
Federer carried the Swiss flag at the opening ceremonies in Beijing in 2008 and Athens in 2004.