The jurors deliberated for eight hours on Wednesday and early Thursday.
Cyr, 34, put his head in his hands and cried as the decision was announced. He had nothing to say as he was led to an RCMP van.
Amanda Trevors, the child's mother, cried out and hugged family members. Throughout the trial she had carried a picture of her daughter, Natalia Shingoose, the victim.
The emotion-packed trial started Jan. 5. Court heard the girl died of blunt force trauma and suffered several injuries. She was found dead in her bedroom June 20, 2012.
The Crown's case was that Cyr assaulted the girl, whom he had been caring for, and she died as a result. The defence argued another man killed the child and Trevors was trying to protect him.
As the jurors left the courtroom, Trevors yelled "Thank you!" to them.
Trevors said she's happy with the decision, telling reporters the jury saw through the defence case, calling it "lies and allegations".
"It was a long three weeks," Trevors added. "I was on the stand for three and a half days and I was trashed on there."
During her testimony, Trevors was quizzed about what she saw when she came home from work June 19 and what happened through the night.
It was Trevors who found Natalia's lifeless body the next morning and called 911.
"Justice is coming," Trevors added. "It's almost finished."
Outside court Thursday, defence lawyer Bob Hrycan told reporters he will file an appeal of the verdict.
"Today, the jury convicted an innocent man," Hrycan said. "They had no physical evidence showing that he did this. They had no motive. The only thing they had was opportunity and other people had opportunity."
Cyr will be sentenced May 1. The sentence for second-degree murder is automatically life in prison with no eligibility for parole for at least 10 years. The judge will set the eligibility period. The jury made no recommendation on that.
Crown attorney Adam Breker, who presented the case along with another Crown lawyer, James Fitz-Gerald called it a challenging case.
"There were no admissions made and there were no eyewitnesses," Breker said. "But we felt, certainly, that after a common-sense review of all the evidence that was available, that clearly Mr. Cyr was the one responsible for this."