Walberg called Pepperdine "a beautiful place" and said, " It just comes down to what I need to do personally and what's best for my family."
Athletic Director John Watson said: "I'm sorry this had to happen like this, but it's more important that he take care of his personal matters at this time."
Assistant Eric Bridgeland was named interim head coach.
Walberg became Pepperdine coach last season. His 2006-07 team had an 8-23 record and this year's squad is 6-12 and 0-2 in the West Coast Conference.
Walberg previously was head coach at Fresno City College.