The 15-year-old, identified only as Boy A, had told his mother that he was staying at a friend's house, but instead was at the apartment of teacher, Rebecca Joynes, where they sex two times.
Ms Joynes, 30, is on trial at Manchester Crown Court accused of six counts of engaging in sexual activity with a child, including two while being a person in a position of trust, all relating to two teenage boys who remain anonymous for legal reasons.
Boy A told jurors he and the teacher exchanged messages and she picked him up on a Friday night after school.
His mother told the court, her son came home from school, changed out of his uniform and packed an overnight bag. He said he was staying at his best friend's house as he had done before. Boy A later told police he had arranged to meet Joynes who took him back to her flat at Salford Quays, where they had sex twice.
The next day, boy A went shopping with his mother, when she noticed a mark on her son's neck, which she said "looked like a love bite".
The defendant claims sexual activity with Boy B did not start until he turned 16. Ms Joynes denies two counts of sexual activity with Boy A, two counts of sexual activity with Boy B and two counts of sexual activity with Boy B while being a person in a position of trust. The trial continues.