The allegations against 30-year-old Ryan Balletto and 24-year-old Patrick Pearmain are outlined in a federal criminal complaint unsealed on Monday.
The men have been charged with marijuana possession and using a minor in drug operations.
Authorities alleged Balletto and Pearmain used the girl to cut marijuana buds at a Lake County property and had sex with her.
According to CBS San Francisco, the girl from the Los Angeles area told investigators she was kept in a 4-by 2-foot box for at least three days right next to a trailer on the pot growers' property.
Authorities reportedly found a noose and a rack to hold someone against their will and several bondage-related sex devices near the box.
Police confiscated over one thousand marijuana plants and a stash of weapons, according to the station.
Police reportedly said the victim is now in a safe place and there is some indication that there may be other victims. Authorities urge those that might have been victims of the two suspects to step forward.