The 2020–21 Pepperdine Waves men's basketball team represented Pepperdine University during the 2020–21 NCAA Division I men's basketball season.

The Waves are led by head coach Lorenzo Romar, in the third season of his second stint after coaching the Waves from 1996 to 1999.

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

They defeated Santa Clara in the quarterfinals of the WCC tournament before losing in the semifinals to BYU.

They defeated Santa Clara in the second round of the WCC tournament before losing in the third round to Saint Mary's.