The 2015–16 Pepperdine Waves men's basketball team represented Pepperdine University during the 2015–16 NCAA Division I men's basketball season.

This was head coach Marty Wilson's fifth full season at Pepperdine.

The Waves played their home games at the Firestone Fieldhouse and were members of the West Coast Conference.

They defeated San Francisco in the WCC tournament to advance to the semifinals where they lost to Saint Mary's.

They advanced to the quarterfinals of the WCC tournament where they lost to Gonzaga.