Police in Quebec say Guy Turcotte surrendered Wednesday just hours after Quebec's top court ordered a new trial in the case.
The Crown said it intended to charge Turcotte, once again, with two counts of first-degree murder.
Police said Turcotte was to be arraigned on Thursday.
Turcotte is the former cardiologist who was charged after his children were repeatedly stabbed one night in February 2009.
He was found not criminally responsible at his 2011 murder trial, when a jury accepted his argument he could not recall the events and had experienced blackouts.
The case made Turcotte a household name in Quebec and the verdict provoked a torrent of outrage.
His case was one of several infamous court decisions that helped spur new federal legislation aimed at making it harder for those found not criminally responsible to gain their freedom.
Turcotte's first trial heard that his young son and daughter were stabbed 46 times.
He was freed after 46 months of detention in a prison and, eventually, a mental institution.
"An arrest warrant was issued today for Guy Turcotte so that he would appear before the courts to answer two charges of premeditated murder," Crown spokesman Jean-Pascal Boucher told reporters.
Boucher said only a Superior Court judge would be authorized to grant any request by Turcotte to be released pending his new trial.
He did not know when the case will be heard, but he insisted prosecutors would work to hold the trial as soon as possible.
The Crown welcomed the decision earlier in the day by Quebec's Court of Appeal with "satisfaction," Boucher said.
The court ruled that legal errors were committed in Turcotte's original trial — including by the Superior Court justice who presided over it.
In the 2011 trial, the jury heard Turcotte drank washer fluid later in the evening of the killings in what he said was an attempt to end his own life. The Crown said a not-criminally-responsible verdict should be reserved only for cases of mental illness, not ones where a suicide attempt might have triggered an after-the-fact blackout.
The appeals court verdict sided with such critics.
"The burden of proof was on the accused to show that he was suffering from an incapacitating mental illness — distinct from the intoxication symptoms — and it was the jury's job to decide," said Wednesday's ruling.
"But the judge did not remind jurors of that distinction."
The appeals court conceded that the judge had a difficult role, and wasn't helped by the fact that the Crown argued its points in a way that was "sometimes confused."
That being said, according to the appeals court, "his instructions (to the jury) were deficient, which necessarily had a major impact on the verdict."
The defence argued during the appeal process that the Crown had plenty of time to raise objections before the jury went into deliberations.
Attorney Pierre Poupart told the court in September that both sides agreed to the parameters of the trial and the Crown knew what was at stake when the not-criminally-responsible defence was introduced.
Poupart argued that the jury came to a reasonable verdict and he stressed it was important for the appeals court to avoid being used as an unofficial 13th juror.
The mother of the two children, Turcotte's ex-wife, told the French-language CBC TV network that she welcomed the appeals court decision to order a new trial as a "necessary evil."
Isabelle Gaston, who has become an outspoken advocate for justice reform, had been bracing herself for the possibility of living through another trial, proceedings that would once again hear the gory details of the killings.
Gaston, who gave the interview before the Crown announced it had issued an arrest warrant for Turcotte, said Wednesday's court decision took her by surprise, at a time when she had finally found inner peace for the first time since the deaths of her young children.
Turcotte's case has already prompted reaction from Ottawa.
Earlier this year, the federal government tabled the Not Criminally Responsible Act. The bill, C-54, would give the court fresh powers to create a new high-risk category that would hold mentally ill offenders longer, without a formal review, and make it far more difficult for them to leave psychiatric facilities.
It would also keep victims' families informed about the status of such individuals and alert them when they are released.
Turcotte's case was one of several highly publicized ones cited by the Conservative government as it introduced the changes. Others included that of Allan Schoenborn, a B.C. man who killed his three children, and Vince Li, who beheaded a man on a bus in Manitoba.