The suspect, 17-year-old Austin Reed Sigg, made his first court appearance Thursday in the death of Jessica Ridgeway and an assault on a 22-year-old female runner in May.
Authorities said Thursday they have "overwhelming" DNA evidence against Sigg.
Sigg lived about a mile from Jessica Ridgeway, who disappeared Oct. 5.
He kept head bowed for much of the time, talking with his attorney but otherwise saying little.
He made eye contact at one point with relatives of Ridgeway, who were in the courtroom wearing purple ribbons in the girl's memory.
District Attorney Scott Storey said the law prevents prosecutors from seeking the death penalty because Sigg is a juvenile, even though he is being prosecuted as an adult.
Police in the Denver suburb of Westminster said they took Sigg into custody Tuesday night after receiving a phone call, apparently from his mother, that led them to Sigg.
Reached by phone, Sigg's mother told The Associated Press he turned himself in.
"I made the phone call, and he turned himself in. That's all I have to say," said Mindy Sigg, before she broke down in tears and hung up.
Authorities said Sigg also will face charges in the May 28 attempted kidnapping of the 22-year-old runner at the Ketner Lake Open Space. Police have said the two crimes are connected but haven't elaborated.
In the May case, a woman fought off a stranger who grabbed her from behind and put a rag that smelled of chemicals over her mouth, authorities said. Police haven't determined if the substance on the rag was meant to subdue the woman.
Authorities have released few details about their investigation, and court documents have been sealed. A police custody report said Sigg was cooperative when he was arrested and waived his rights.
Acquaintances have said Sigg was interested in mortuary science and forensic science, often wore black and hung out in the high school cafeteria's "goth corner."
Sigg had attended Witt Elementary, but he moved on to middle school in 2007, before Jessica enrolled at Witt, Jefferson County Public Schools spokeswoman Lynn Setzer said.
Sigg later attended Standley Lake High School while also taking classes at Warren Tech, a district school that offers specialized training in health science, public safety, technology and other fields.
He left the school district in July after finishing the 11th grade and later earned a GED. School officials don't know why he left.
Arapahoe Community College officials confirmed Sigg is enrolled there but wouldn't release other details.
As technicians in white coveralls searched Sigg's home, former high school classmates painted a picture of Sigg as an intelligent teen who often wore black and complained about school but who would stay late sometimes to work on computers.
Sigg was interested in mortuary science and was taking forensics classes, said Rachel Bradley, 17, who attended Standley Lake with him. Arapahoe Community College offers the state's only accredited mortuary science program.
"It's just so weird to grasp the concept of how, like, I knew him and how he lives so close to us," Bradley said Wednesday.
"I never saw it coming," she said of the allegations against Sigg.
Yearbooks showed Sigg was a member of the choir in his freshman and sophomore years.
Former schoolmate Sarah Morevec said Sigg had been bullied for having a high voice.
Dakota Foster graduated from Standley Lake in 2011, a year before Sigg left. Foster on Wednesday said he and his friends sat at the opposite end of a cafeteria table from Sigg and his friends.
"He was really nice and laughed a lot with us and told jokes, and laughed at our jokes," Foster said.
Foster, 19, said he didn't know Sigg well, but "he used to hang out with a lot of us in what we called the goth corner (of the school cafeteria), where all the metal heads were."
"He wore all black so he fit it," Foster said. He added he wasn't surprised that Sigg left high school after the 11th grade.
"I know he didn't like his classes very much," Foster said. "He always complained about school."
Neighbor Brooke Olds, 13, said Wednesday she usually saw Sigg alone on a skateboard or scooter.
"He was shy and kept to himself," she said.
Police said they notified the Ridgeway family of the arrest Wednesday morning. Jessica lived in Westminster with her mother, Sarah Ridgeway. Jessica's father, Jeremiah Bryant, lives in Missouri.
Jessica's great-grandmother Donna Moss told Kansas City-area reporters that she feels for Sigg's mother but has to fight the rage she has toward Sigg because she knows as a Christian she should forgive.
"I think it's all I've got within me to not want to just burn him, and I mean burn him," she said.
The arrest brought some relief to the community, where some parents said they were nervous about letting their children play outside as authorities searched for Jessica's killer.
"Every parent in every Colorado community will rest a little easier tonight," said Gov. John Hickenlooper, who has a 10-year-old son, Wednesday. "While we still mourn the death of Jessica Ridgeway, we are relieved an arrest has been made and the pursuit of justice can continue."
Elliott reported from Denver. Associated Press writer Kristen Wyatt in Denver contributed to this report.