Her parents say 13-year-old Nicole Lovell pushed a dresser against her bedroom door and climbed out a window in her Blacksburg, Va., home when they saw her for the last time last Tuesday.
Lovell's body was found late Saturday afternoon in Surrey County, North Carolina.
Police first charged freshman student athlete David Eisenhauer from Maryland with her murder on Sunday, as he was already being held under suspicion he'd been involved in Lovell's abduction.
Later Sunday, police announced a second arrest: Virginia Tech freshman Natalie Keepers, a 19-year-old fellow Maryland native.
It's not clear how Eisenhauer and Keepers know each other. Eisenhauer is from Columbia, Md., and Keepers is from Laurel, Md., according to police.
She is being charged with helping the former track athlete dispose of Lovell's body, and being an accessory to a felony after the fact.
On Friday, Nicole's father posted a message to Facebook.
"Nicole, honey, if you see this if you're out there you can come to me. I'm not mad at you. I'm worried about you. Your family is worried about you. Just come home," he said.
Police have so far only said that Eisenhauer and Nicole "were acquainted" prior to her disappearance, and that he "used this relationship to his to abduct the 13-year-old and then kill her."
CBS News' Jericka Duncan reports that Nicole's Facebook page shows she was a member of at least one teen dating group.
But it's unclear whether she met Eisenhauer online.
Last March, the track and field state champion was recognized as Student Athlete of the Week by a local news station.
"I personally will not stop until I reach my peak performance," Eisenhauer said during the interview with the station.
Lovell's body is being returned to Roanoke, Va., for a medical examination.