The assault occurred when Owen Labrie, 18 at the time, participated in a school tradition of older students competing for sexual conquests.
Labrie, who is now 20, was charged with rape but later convicted of a misdemeanour sexual assault.
He was also found guilty of using Facebook and email to lure the girl.
His case brought into the spotlight the St Paul's School tradition called "Senior Salute", in which older pupils kept a score of how many girls they had sex with.
He had said he and the girl, now 17, had consensual sexual contact but he stopped short of raping her in a moment of "divine intervention".
In trial, he admitted to bragging about having intercourse with her in an academic building to his friends.
The girl said she has been verbally assaulted by other students since returning to school and has been "living in almost constant fear".
Prosecutors had asked for three to seven years in prison while Labrie's defence called for probation and community service, characterising the encounter as a consensual act between two teenagers.
Superior Court Judge Larry Smukler called Labrie a "very good liar" as he sentenced him.
A man has been sentenced to a year in jail for sexually assaulting a 15-year-old girl at an elite prep school in New Hampshire, where they were students.