The family of Ann Maguire, 61, were in the courtroom in Leeds for the first appearance of the youth, who cannot be named for legal reasons.
The boy, whose right arm was in plaster, spoke only to say “yes” in response to questions from an official at the special youth court and nodded to his own parents.
The teacher’s husband Donald stared at the youth as he was led into the glass-fronted dock, and clutched the hands of his two daughters during the two-minute hearing.
Ann Maguire, who taught Spanish, suffered multiple stab wounds in the incident on Monday at Corpus Christi Catholic College in Leeds.
The youth was arrested at the scene and charged with murder on Wednesday.
He will appear again at a higher court on Friday.
The teacher’s family earlier paid tribute to Maguire, who was months from retirement, as their “shining light”.
“She brightened the world for so many of us,” they said in a statement released through police.
“A loving wife, the best mother, a treasured sister, a true friend. This horrific happening has robbed us of all of this and so much more.”
They said they were “overwhelmed” by the support they had received.
Prime Minister David Cameron’s spokesman meanwhile supported local calls for a permanent memorial to be erected to the teacher, saying it would be “fitting”.
Violence at British schools has risen in recent years, and there has been growing concern over knife attacks involving teenagers.
But it is the first case in which a teacher is alleged to have been killed by a pupil in a classroom.