Labrie, 19, a former student at the elite St. Paul's School, appeared shaken as the verdict was read, at one point nodding his head and reaching for a tissue to wipe tears.
At the time of the assault, the accuser was 15 and Labrie was an 18-year-old senior.
In the end, the jury did not appear to believe the former prep school student's claim that there was no intercourse, but it also seemed to dismiss his accuser's testimony that it was against her will, CNN legal analyst Sunny Hostin said.
Labrie was convicted of a felony charge and four misdemeanors: the most serious count being the use of an online service or the Internet to seduce, solicit or entice a child under age 16 in order to a commit sexual assault. He also was convicted of three counts of misdemeanor sexual assault and child endangerment.
At his October 29 sentencing, Labrie faces a maximum sentence of 11 years. Labrie, who will have to register for inclusion on the sex offender list, was released on bail under a 5 p.m. to 8 a.m. curfew.
He was acquitted of the more serious counts of aggravated felonious sexual assault -- punishable by 10 to 20 years in prison -- as well as simple assault, a misdemeanor.
There were no winners in the case, Hostin said.
"In New Hampshire, forcible rape -- the requirement to have force -- is not an issue," she said. "It's only consent. And so the jury clearly did not believe that she did not consent and that's why we have the felonies tossed out. Let's be clear, those were the most important charges for this prosecution."
Labrie's conviction, however, ensures that he's added to the sex offender registry, Hostin said.
"That's a problem with these sex cases," she said. "We have to look at them a little bit differently because no does mean no, and no is not necessarily a word, 'no' can be an action. Our sex laws really need to evolve."
The jury, made up of nine men and three women, deliberated for 7½ hours.
"In essence, what happened as a result of this trial is one teenager was found guilty of having consensual sex with another teenager," Labrie's lawyer, J.W. Carney, said after the hearing.
He said the internet-related charge was actually intended to prosecute people who disguise their age and try to lure unsuspecting children into sexual encounters, not people like his client.
"I believe that this computer statute was never intended for kids getting together consensually at the high school they both attend," he said. "It's overreaching."
The victim's family said: "A measure of justice has been served for victims of sexual violence. While he was not convicted on all charges, Owen Labrie was held accountable in some way by a jury of his peers for crimes he committed against our daughter."
"This conviction requires him to take ownership for his actions and gives him the opportunity to reflect upon the harm he has caused. There is no joy in this outcome, however, as our daughter can never get back what she has lost nor can St. Paul's School ever be our community again."
In the statement, the family said it felt "betrayed that St. Paul's School allowed and fostered a toxic culture that left our daughter and other students at risk to sexual violence. We trusted the school to protect her and it failed us."
St. Paul's Rector Michael G. Hirschfeld, in a statement, commended the "remarkable moral courage and strength demonstrated by the young woman who has suffered through this nightmare."
"Her resolve and unwavering commitment to the truth have been inspiring to us and to many outside our School community. We can only hope that time will bring some measure of healing and comfort to both her and her family. The entire St. Paul's School community has been deeply affected by this incident. It is our responsibility to ensure that our students live and learn together in a community that is built on respect, caring, and support for one another. Anything short of that cannot and will not be accepted."
On Wednesday, Labrie -- with his accuser watching in the courtroom -- took the stand and described the encounter last year as consensual. He said the two of them sneaked into an attic room in a St. Paul's School academic building a few days before graduation and together spread a flannel blanket Labrie had brought with him.
In closing arguments, prosecutor Joseph Cherniske told the jury that the defendant carefully planned out a sexual assault and viewed the taking of the girl's virginity as a source of pride.
"It wasn't the school's fault," he said, rebutting the defense argument that St. Paul's encouraged a tradition known as the "Senior Salute" in which seniors sought to have sexual encounters with younger students.
Carney accused St. Paul's of allowing the "Senior Salute" to flourish.
"The idea that you would wink at a tradition that 'Senior Salute' represents is shocking," he said, denying that his client sexually penetrated the girl.
"It damages children and in this case it damaged both (the accuser) and Owen," he said. "When you saw the culture of St. Paul's, it was one that encouraged, I submit, the concept of 'Senior Salute.' In fact, it was so revered on the campus it became a tradition."
In a statement to the "St. Paul's School Community," Hirschfeld and James M. Waterbury, president of the school board, denied that the "Senior Salute" was a tradition at the 159-year-old prep school.
"The phrase 'senior salute' describes a wide range of behaviors," the statement said. "It was never understood to include the conduct engaged in by Owen Labrie. That behavior was never condoned by the School, and we took action when it surfaced."
The statement said Labrie was banned from the school and his rector's award was rescinded. In addition, the student handbook was revised to "state more explicitly that participation in any 'game' of sexual conquest by any name ... would be grounds for expulsion."
The trial has brought unwanted attention to the elite school
, the alma mater of Secretary of State John Kerry and half a dozen congressmen.
On Wednesday, Labrie testified that sweatshirts, shirts and later pants were removed but the two kept their underwear on.
When a defense attorney asked about their demeanor, Labrie testified they were both giggling and smiling and that the girl held him in an affectionate way.
"I thought she was having a great time," he said.
Labrie, 18 at the time, said he may have gotten carried away at times, leading to bruises she reported on her breasts. They were both aroused, he said, so he went to put a condom on, but he stopped himself.
"It wouldn't have been a good move to have sex with this girl," he told the court. "It would not have been a good choice for me to make."
The liaison awkwardly ended after a few more brief kisses, and Labrie hurried to a choir concert, he said.
The accuser, now 16, testified last week
that Labrie penetrated her with his fingers before raping her.
"I was raped!" she said when a defense attorney suggested she had sent conflicting signals to the defendant.
The defense depicted Labrie as a great student, on a full scholarship, who wanted to attend Harvard, take divinity classes and perhaps become a minister.
The prosecution repeatedly questioned him about telling friends after the encounter that he had sex with the girl.
He was bragging and lying, Labrie told the court.
He also said for the first time that his boxers were damp and he may have ejaculated on them before he put on a condom. He didn't tell police about it, he said, because their questions focused on whether the two had sex.
"This was a very difficult case because of Owen's own statements to his friends," defense lawyer Carney said after the trial. "I think the critical evidence was not the testimony of the complainant, it was the testimony of Owen given when he was talking to his friends and acting like a teenager who didn't want to say he had been unsuccessful in his 'Senior Salute.' "
State criminalist Katie Swango said semen and sperm were found on the young woman's underwear. Further testing of sperm cells found on the underwear were inconclusive. However, some of the biological material found on the underwear matched Labrie's DNA, she said.
Another state criminalist, Kevin McMahon, said he examined a swab from the accuser's cervix and found no evidence of sperm.