They were charged after appearing in a video mocking Muslim prayers.
The 30-second video showed the students pretending to pray, with one kneeling on the floor while reciting Qur'anic verses and two others standing behind him and laughing.
One waved his hand under a second's neck in a sign of beheading.
The video was filmed by the students' teacher, who is also a Christian, and who was sentenced to three years in prison for insulting Islam, in a separate trial.
While the teenagers didn't appear in court, ten security trucks surrounded the building.
It's reported that the families of the students cried, and some women wailed in disbelief and collapsed on hearing the verdict.
Their lawyer Mr Naguib described the ruling as "unbelievable" and said the judge should have just punished the teenagers with a fine.
The video came to light in April 2015 just after Islamic State extremists beheaded dozens of Coptic Christians in Libya.
The video led to the homes of the students being attacked by locals and the village elders asking them to leave.