Mary Gowans, 43, was charged with sexual assault and sexual interference for alleged incidents in 2010 involving a 15-year-old male student who is now 18.
Justice John McMahon ruled Friday there were too many inconsistencies in the testimony he heard, and found the former French teacher not guilty on both charges.
The case was heard by judge alone.
The judge said the teen's evidence was inconsistent with earlier statements to police. He called those inconsistencies "significant and troubling."
Judge McMahon later said he couldn't be certain of the teen's version of events and said the Crown had not met the burden of proof.
Teacher quits job over allegations
During the trial, the court heard that the pair often spent time alone together outside the classroom. He babysat her children and they frequently went running together.
Gowans testified she did not engage in an inappropriate sexual relationship with the former student, who cannot be named under law.
The former French teacher said the allegations and charges against her destroyed her life.
"After the arrest in 2010, obviously that caused a great deal of stress in our family," Gowans told the court.
She quit her job on the advice of her union, she said.
"I didn't feel I had any choice. My life had been destroyed on every possible level," she said.
Gowans also said the allegations broke up her marriage.
Faces college of teachers hearing
Outside the court on Friday, Gowans spoke briefly to reporters.
"Obviously I'm very glad that this is over today," she said. "The last three years of my life have been virtually destroyed as a result of these allegations. And I'm glad it's over, but at the same time I have the task of rebuilding my life now."
Gowans's lawyer said her reputation has been so badly damaged that she may never recover.
And her troubles may not be over. She may still face a disciplinary hearing from the Ontario College of Teachers.
A representative who was in court on Friday said the burden of proof for misconduct is not as high for the college as it is in the courtroom.Suggest a correction