The 2012–13 Pepperdine Waves men's basketball team represented Pepperdine University during the 2012–13 NCAA Division I men's basketball season.

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

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

They lost in the second round of the WCC tournament to San Diego.

Sources: All non-conference home games, and conference home games not picked up by the WCC regional packages, are shown on TV-32 in Malibu, known as Pepperdine TV.