The arrests came on Saturday after police, following a four-day search, found the remains of Nicole Lovell in North Carolina, about 90 miles (145 km) south of Blacksburg, Virginia, where her home and the university are located.
Lovell had been missing from her family's home since Wednesday. A family member told the Roanoke Times it appeared she had climbed out of a first-floor window.
It was not immediately clear how she crossed paths with David Eisenhauer, 18, a freshman from Columbia, Maryland, and member of the university's cross-county team.
But police in Blacksburg, about 40 miles (64 km) west of Roanoke, Virginia, said investigators had determined the two teens became acquainted before her disappearance. Eisenhauer took advantage of that relationship to abduct and kill Lovell, they said in a statement.
Police have not said how Lovell died.
A star Maryland high school athlete before coming to Virginia Tech, Eisenhauer was named the Howard County Times/Columbia Flier Indoor Track Athlete of the year, according to a 2015 profile in the Baltimore Sun.
Natalie Marie Keepers, 19, a sophomore at Virginia Tech from Laurel, Maryland, was arrested on Sunday and charged with improper disposal of a dead body and accessory after the fact in the commission of a felony.
"I'm so in shock I know nothing more to say," the victim's father, David Lovell, said on Facebook. "I'm broken!"Family members had pleaded for Nicole Lovell's return, saying she was without the prescription medicine she needed daily after undergoing a liver transplant.
Authorities said they were working to piece together the events leading to Lovell's death.
A Virginia Tech spokeswoman would not comment on the enrollment status of Eisenhauer and Keepers, but the university said in a statement it had the authority to suspend students immediately on an interim basis in the case of a felony arrest.
Hundreds of students in the university's Corps of Cadets, along with students and researchers using drones, assisted in the search for Lovell, the school said.