The computer was reported missing Tuesday by Lincoln B.P. Management Inc., which helps manage base housing.
The company and Camp Pendleton are investigating. As of Friday, investigators had not found evidence that the data had been accessed, the base said in a statement.
Authorities would disclose what kind of information was on the computer.
Lincoln B.P. officials were notifying residents.
"We take this matter very seriously and are working closely with Lincoln Properties to find out what happened and to safeguard the personal information of our Marines, sailors and their families," said Col. James B. Seaton III, the base's commanding officer.
Camp Pendleton is the Marine Corps' largest West Coast expeditionary training facility, located north of San Diego.