Pedro Hernandez has been found guilty for the 1979 murder and kidnapping of Etan Patz.
The verdict was handed down by a jury around noon Tuesday, nine days after the began deliberations in the case.
Hernandez, 56, was convicted of felony murder and acquitted of intentional second-degree murder by the jury, meaning that the jury believed he did mean to kill the boy.
The convicted killer, who is now facing a possible sentence of life in prison, showed no signs of emotion as the jury read out their verdict on today.
Etan, 6, vanished while walking alone to school for the very first time on May 25, 1979 and his face was one of the first on milk cartons.
His body has never been found.
Etan's father Stan openly wept in court as the verdict was read aloud, and was comforted by some of the jurors from the last trial who came to hear the verdict.
Many of those individuals were in tears as well when they learned that Hernandez had been found guilty.
He also took time to hug members of the district attorney's office and in a statement afterwards thanks those people who offered their help and support in the case over the past four decades.
"The Patz family has waited a long time, but we've finally found some measure of justice for our wonderful little boy, Etan,' said an emotional Stan on Tuesday.
"I'm really grateful that this jury finally came back with which I have known for a long time - that this man, Pedro Hernandez, is guilty of doing something really terrible so many years ago."
He later added: "It's about time."
The current jury's foreman also spoke out after the verdict saying that the group "had constructive conversations, based in logic, that were analytical and creative and adaptive, and compassionate."
Hernandez confessed to the murder and kidnapping of the Etan in 2012 after the case made national news again when federal agents dug up a New York City basement looking for Etan's remains.
He had been tried once before, but the case ended in a hung jury after all but one member voted to convict Hernandez after 18 days of deliberations.
Over the years, Hernandez told a friend, his ex-wife and a church group that he had killed a young person in New York by choking and dumping the body, though the details varied, according to trial testimony.
Hernandez never mentioned Etan by name, but his brother-in-law called police with the tip that led law enforcement to him five years ago.
That was when he confessed to the boy's death.
Hernandez told police that he offered Etan a soda to get him into the basement of the store where he worked and then choked him before putting him in a box which he left with a pile of curbside trash.
Etan was still alive at the time according to Hernandez.
"Something just took over me," he told police.
Defense lawyers and doctors portrayed Hernandez as man with psychological problems and intellectual limitations that made him struggle to tell reality from fantasy.
They claimed that these conditions made him susceptible to falsely confessing to the murder of the child after more than six hours of questioning.
Hernandez's daughter testified that he talked about seeing visions of angels and demons and once watered a dead tree branch, believing it would grow.
"Pedro Hernandez is an odd, limited and vulnerable man," stated defense lawyer Harvey Fishbein in his closing argument.
"Pedro Hernandez is an innocent man."
Fishbein also said that he planned to appeal the case, telling reporters: "In the end, we don't believe this will resolve the story of what happened to Etan back in 1979."
Prosecutors meanwhile said that Hernandez faked and exaggerated his symptoms.
Manhattan District Attorney Cy Vance also released a statement on Tuesday, saying: 'The disappearance of Etan Patz haunted families in New York and across the country for nearly four decades.
"Etan's legacy will endure through his family's long history of advocacy on behalf of missing children. However, it is my hope that today's verdict provides the Patz family with the closure they so desperately deserve."