The French 15-year-old now faces prison time for the "joke" which took place in a Paris classroom last week.
He can be heard shouting "put your head down" in the clip as though he's about to execute the terrified woman.
Others filming the incident can be heard laughing after the gun-wielding teen barged in on the teacher marking work at Branly High School.
The video went viral when it was shared online on Friday, sparking widespread outrage across France.
After seeing the horrifying footage, President Emmanuel Macron ordered the interior ministry to "take all measures to ensure that what happened is punished, and that this type behaviour is permanently banned from schools."
The teacher in the clip reported the schoolboy for "violent threats with a weapon" which can be punished by up to five years in prison.
Following her complaint, the boy handed himself in to cops by turning up at a police station with his father.
He told a youth judge on Sunday that he had not intended to intimidate the teacher with the fake pistol, and that he was just enjoying a joke.
But the charge could still stick if the court deems that the fake gun was used if it was real.
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