Two men accused of first-degree murder in the fatal shooting of Jordan Manners were found not guilty on Thursday, nearly four years after the Grade 9 student died.

Manners was shot inside C.W. Jeffereys Collegiate Institute. It was the first-ever fatal shooting inside a Toronto high school.

Two men known only as C.D. and J.W. were charged with first-degree murder in the death. They were released from custody on Thursday, after the jury sided with defence's assertions that the death was an accident between friends.

"This is a tragedy that cost Jordan Manners his life and cost these boys four years of their lives," C.D.'s lawyer James Silver told reporters. "They lost their friend. What are they going to do now? They are going to try and put their lives back together and move forward."

Jurors began deliberating on Wednesday, the day Manners would have turned 19 if he were still alive. He was shot with a .25-calibre bullet on May 23, 2007.

The not guilty verdict was announced Thursday afternoon, surprising many inside Toronto's University Avenue courthouse.

A loud shriek came from the gallery as the verdict was delivered and one woman was escorted from the room.

The two accused each turned and hugged their lawyers.

Crown prosecutor Tom Lissaman said he would respect the decision of the jury and would not file an appeal.

"In the manner that this evidence came out in front of this jury, it is a reasonable verdict and we thank them for the service that they gave to this community on a very difficult case," Lissaman told reporters.

The Crown had alleged that C.D. and J.W., who cannot be identified because they were 17 at the time of the shooting, killed Manners during an attempted murder.

Defence lawyers had argued that Manners shot himself accidentally as he examined a gun in the school's second-floor washroom.

They said that the two accused in Manners' death were friends with the victim and had no reason to murder him.

"These were friends of the young man, Jordan Manners," said J.W.'s lawyer Donald McLeod. "These men have been in custody since they were 17. They have been in custody for four years; they have lost a lot of their lives."

One of Manners' teachers testified that the student had a fascination with guns. Evidence was also presented that a photo of ammunition was found on Manners' cellphone.

Prosecutor Tom Lissaman said no gun or shell casing was found at the scene.

Lissaman played a videotaped statement from a former student telling police she saw J.W. drag manners down the stairwell. When she appeared in court, the witness said she made the story up to get attention.

Toronto Police Det.-Sgt. Michael Barsky said it was frustrating and disappointing to hear a witness recount her original testimony, suggesting the justice system had been "hijacked."

"Our belief is that the two people responsible for this just faced a trial of their peers and their peers found them not guilty," said Toronto Police Det.-Sgt. Michael Barsky. "We do not believe for one minute that the wrong people were arrested."

This was the pair's second trial. The first ended in a hung jury and a mistrial last year when two witnesses changed their stories from what was originally given to police.

One young girl said she could not remember what had happened; while another said her account had been based on gossip.

The retrial began in March, with the two accused, now 21 years old, restating their pleas of not guilty.

Manners' death sent shockwaves through the city in 2007. The teen, described as sweet by neighbours in a housing complex, had celebrated his 15th birthday just days before the fatal shooting.