The 2016–17 Pepperdine Waves men's basketball team represented Pepperdine University during the 2016–17 NCAA Division I men's basketball season.

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

The Waves played their home games at the Firestone Fieldhouse in Malibu, California as members of the West Coast Conference.

They lost in the first round of the WCC tournament to Pacific.

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