Kelsey Peterson's court-appointed attorney argued for $100,000 bail, but a federal magistrate judge in El Centro ruled she was a flight risk.
Peterson showed no emotion as she told the judge that she agreed to be transferred. She smiled weakly at her attorney when she left the courtroom.
The 13-year-old who fled from Nebraska with Peterson told The Associated Press his friendship with the teacher led to sex.
"I had problems in Lexington and I wanted to get away, but it was a bad idea," he said in an interview Tuesday at a home in Janitzio, Mexico, where he is staying with a family friend temporarily. "Now I can't go back."
The boy immigrated illegally to the U.S. when he was much younger and speaks little Spanish. He shed no tears while Peterson wept as the two parted Friday night at a police station in the border city of Mexicali, according to the Mexican official who captured the pair.
"She said to the youngster that she loved him and would always love him in her heart," said Alfredo Arenas Moreno of the Baja California state police.
The boy said the trip was Peterson's idea, but he went along with it.
He said he had sex with the teacher while they were in Lexington, Nebraska, a meatpacking town that has seen a large influx of Mexican immigrants.
"It didn't happen that many times," he said. "It happened maybe twice, I think."
The boy called his former teacher "my best friend" but said she was not his girlfriend.
The AP had previously named the boy but later removed his name because the most recent charges allege he was the victim of a sex crime.
Peterson is charged with taking a minor across state lines with the intention of having sex with him.