David Eisenhauer, 18, has been charged with kidnapping and first-degree murder in the death of Nicole Madison Lovell, who had endured a liver transplant and bullying at school and online.
Her body was found Saturday in North Carolina, four days after she left home, police said.
Natalie Keepers, 19, faces charges of improper disposal of a body and accessory after the fact in the commission of a felony.
Eisenhauer appeared briefly in court, out of sight of reporters, ahead of the scheduled 10 a.m. hearing. Eisenhauer retained a court-appointed attorney, the clerk's office said.
Keepers also appeared, handcuffed and shackled, in an orange jumpsuit. She told Judge Robert Viar Jr. that she understood the charges and that she had also retained counsel. Her next court date is March 28.
Police said they have evidence showing Eisenhauer knew Nicole before she disappeared, but have not said anything about a possible motive. Nicole's family said she apparently blocked her bedroom door with furniture and climbed out a window Wednesday night.
"Eisenhauer used this relationship to his advantage to abduct the 13-year-old and then kill her," a Blacksburg police statement said. "Keepers helped Eisenhauer dispose of Nicole's body."
Authorities said they located the girl's remains on Saturday in Surry County, N.C., just over the Virginia border.
Blacksburg Police Chief Anthony Wilson told the Roanoke Times that Eisenhauer has not confessed and did not provide information that led to Nicole's body.
A state police search and recovery team has been searching a pond on the Virginia Tech campus, but state police spokeswoman Corinne Geller would not say what they were looking for.
Nicole's life was not easy, her mother, Tammy Weeks, told the Washington Post. She survived a liver transplant, a drug-resistant staph infection and lymphoma when she was 5, Weeks said.
"God got her through all that, and she fought through all that, and he took her life," Weeks said.
Nicole didn't like going to school because girls called her fat and talked about the scars from her transplant, and she often cried to stay home, Weeks said.
"It got so bad I wouldn't send her," Weeks said, but the bullying continued on social media.
She loved pandas and pop music and wanted to be on "American Idol" when she got older, her mother said.
Davy Draper, a close family friend who knew the teen most of her life, called her an energetic and outspoken girl who got along with everyone.
"She was an awesome little girl. She was an angel here on Earth, and she's an angel now," Draper said Sunday.
Both Eisenhauer and Keepers, who came to Virginia Tech from Maryland, were being held without bond at the Montgomery County Jail.
Eisenhauer was a standout track and field athlete in high school, and was named Boys Indoor Track Performer of the Year by the Baltimore Sun in March. The Sun said Eisenhauer had moved to Columbia, Md., from Yakima, Wa., for his junior year and quickly became a star on the East Coast. His coach told the newspaper that Eisenhauer was "the best-kept secret in Maryland."
Both Eisenhauer and Keepers enrolled as freshman engineering majors at Virginia Tech, where hundreds of students and researchers had joined the search for Nicole's body. Eisenhauer has been suspended from the university, according to a Virginia Tech statement.
A number listed for Eisenhauer's parents rang busy. A message left at Keepers' home in Laurel, Md., was not immediately returned. Nicole's family members did not immediately return messages seeking comment.