Nelson County Commonwealth's Attorney Anthony Martin said Randy Allen Taylor, 48, faces charges of first-degree murder, murder during commission of abduction and abduction with intent to defile, the (Lynchburg) News & Advance reported.
Taylor is scheduled for a Feb. 3 trial on an earlier abduction charge in the case.
Murphy was last seen Aug. 3 at a gas station in Lovingston. Authorities say a strand of the Nelson County girl's hair was found in Taylor's home in Lovingston.
Michael Hallahan, Taylor's attorney, has said Murphy and a black male were in Taylor's home but left.
The girl's disappearance has also been investigated by the FBI and Virginia State Police.
A judge last month approved Martin's request for a gag order in the case.