Walberg spent the last four years as head coach for Fresno City College, where he had a 133-11 record. Last season, Fresno City went 34-0 and captured the California State Championship.
He replaces Paul Westphal, who left the program in March after a 7-20 campaign with the Waves last season.
"After a thorough national search in which we interviewed several quality candidates, I am happy to announce the hiring of Vance Walberg as Pepperdine's new head men's basketball coach," said Athletic Director John Watson. "He has a proven track record of developing winning programs at both the high school and junior college levels."
Walberg was named California Junior College Coach of the Year in 2003 and 2005. Prior to going to Fresno City College, Walberg spent 13 years at Clovis West High School.