The boys, all 16, were taken into custody at two high schools, the Los Angeles Times reported Friday.
Officials with the Los Gatos-Saratoga school district said they were fully cooperating with authorities.
Audrie Pott, a high school sophomore, was allegedly assaulted by the youths last fall. She hanged herself eight days later after photos of the assault were circulated on cellphones.
Robert Allard, an attorney representing the girl's family, said she had posted on Facebook before her death that her life was "ruined" and that she had experienced the "worst day ever."
The family has created a foundation in Audrie's memory to award scholarships to students.
"It would have been her wish that we could all learn from her unfortunate and tragic passing that somehow through the lessons learned that this tragedy could provide an impetus for change," the foundation says on its website.
2014: The Year in Music [PHOTOS]