Douglas Parr attends mainstream classes at Comberton Village College in Cambridgeshire.
His mother Kate Bourne said no consent was requested from parents for the 15-certificate film to be shown and the scene had made her son sick.
Mrs Bourne has accepted an apology from the teacher.
The school said it was "very regrettable" that the pupil found the film distressing and added it was "reviewing this particular scheme of work".
The famous scene from the 1960 Hitchcock film shows Anthony Perkins, as the troubled Norman Bates, stabbing Janet Leigh through a shower curtain.
'Sensitive to noises'
In the email to Mrs Bourne, the teacher said the clip had been used to illustrate how music was integral to the mood of a film - but it would not be used again.
Mrs Bourne said: "Dougie came flying through the door after school on Monday saying, 'I had to watch the bloody shower scene from Psycho in music, today'."
He then told her he had been sick.
"Dougie is quite sensitive to noises, so even if his teachers had just played the soundtrack it might have distressed him," Mrs Bourne said.
Douglas's teaching assistant had made a note in his school diary - which details work the pupils have done during the day - informing his mother that he had been upset by a film.
She had removed him from the classroom and he had been sick, the note said.
Mrs Bourne emailed the school, saying: "I cannot for the life of me understand why this has been shown.
"The film carries a certification of 15 years. Dougie is 13.