Brooks is accused of groping an unconscious woman during a late-night gathering at former teammate Ray McDonald's house in December.
A woman claims she was intoxicated when she fell and hit her head on McDonald's hot tub before passing out. The woman claims Brooks groped her and then McDonald raped her. McDonald pleaded not guilty to rape charges on Friday.
The woman filed a sexual assault lawsuit against Brooks earlier this year.
McDonald was released by the 49ers. Brooks remains on the team and appeared in all three games this year.
Brooks' attorney entered the plea in Santa Clara County Superior Court Tuesday. Brooks didn't attend the hearing.