Tammy Marquardt was convicted of second-degree murder in the death of her son Kenneth and handed a life sentence in 1995. (Colin Perkel/Canadian Press)

A mother who spent almost 14 years in prison for killing her toddler has had her conviction quashed after Ontario's top court found flawed evidence from disgraced ex-pathologist Charles Smith helped convict her.

Three Ontario Court of Appeal judges said Thursday Tammy Marquardt has been through a "tragic ordeal" and ordered a new trial. Both prosecution and defence agreed her conviction in 1995 in the death of her two-year-old son Kenneth Wynne, who had epilepsy, was faulty.

"Finally the nightmare's coming to an end and I'm waking up," Marquardt said outside court after the ruling.

But Marquardt still faces a new trial, and the Crown said in court a jury could still convict her because she had motive and opportunity to kill her son. But Crown lawyers didn't say explicitly whether they would pursue the case.

"That's their opinion. I don't buy it for a second," said Marquardt's lawyer, James Lockyer.

The Ontario Ministry of the Attorney General said the Crown will set out its position in open court as the matter proceeds.

Marquardt's conviction was based in part on testimony provided by Smith.

Court heard Thursday that Smith's conclusion that the boy could not have died from an epileptic seizure and was strangled or smothered was misleading and erroneous.

After she was convicted in 1995, Marquardt lost custody of her two other children.

"Try having your heart ripped out and someone squeezing it right in front of your face," she said. "There [are] no real words for it. It's just a lot of pain and hurt that cannot be fixed."

Marquardt, 38, who was living in Oshawa, Ont., at the time, has always maintained her innocence. She was released on bail in March 2009 after a public inquiry discredited Smith's work in a litany of criminal cases. Thirteen of those cases resulted in convictions.

Smith was recently stripped of his medical licence after admitting to professional misconduct and incompetence.

With files from CBC's Mike Crawley and The Canadian Press