Nicole Madison Lovell was last seen between 7 p.m. and midnight Wednesday at her home in Blacksburg, Virginia, police said.
The family found a dresser pushed against her bedroom door and said the middle-school student probably climbed out the apartment window, according to the Roanoke Times.
The family was extremely worried because Lovell required daily prescription medication for a liver transplant and didn't carry the medicine with her, according to police in Blacksburg, Virginia.
The search ended Saturday afternoon when her body was found about 100 miles away from home, Blacksburg Police Chief Anthony Wilson said.
Freshman engineering major arrested
"We were able to determine an approximate area where she might be found," he said. "Virginia State Police were dispatched to the general area Saturday afternoon and she was located just inside the North Carolina border on Route 89 in Surry County."
David E. Eisenhauer, 18, of Columbia, Maryland, was already in custody. He was arrested Saturday morning at his residence on campus and charged with felony abduction, police said. Police said they acted on tips and social media to identify him..
After the remains were found, he was charged with murder. He's being held without bond in a jail in Montgomery County, Virginia, Wilson said.
"The speed at which this investigation has moved today has been nothing less than incredible," Wilson said. "We owe that to the outpouring of support and tips from the Blacksburg, Christansburg and Montgomery County communities."
Eisenhauer is a freshman engineering major and has been a member of the Virginia Tech cross country team, the Roanoke Times reported. The university said he's been suspended.
Police didn't give a motive or say how Lovell died.
CNN is attempting to find out if Eisenhauer has retained an attorney.
"We still have a great deal to do," Wilson said. "
'Very wounded folks'
Lovell's disappearance had gripped the picturesque town of about 40,000 people, where the university is located.
"I'm scared to death," her father, David Lovell, told CNN affiliate WDBJ before she was found.
Police, the family and members of the Virginia Tech Corps of Cadets searched for the girl, according to a statement from the school. Wilson said Lovell's body will be returned for an autopsy and authorities will work to reconstruct a timeline leading up to her death.
"The entire Virginia Tech community extends its support to Nichole's family and friends," the university said in a statement. "The university is also reaching out to our campus community and the greater New River Valley community who may be affected by the events that have occurred over the several days."
Wilson said the Blacksburg community is reeling from the girl's death.
"We have some very wounded folks in this community and and please show them some respect," he said to reporters. "We will continue to be very transparent with you during this investigation but please remember these are the kinds of crimes that rip communities apart."
CNN's Joshua Berlinger and Carma Hassan contributed to this report.
