McCarney, 33, from Trillick in Co Tyrone, was given the life sentence tariff and ordered to sign the sex offenders register on Friday.
In outlining his sentencing, Mr Justice Stephens said he accepted the prosecution's case for a higher starting point of 15-16 years for the murder of a child.
The jail term handed out to McCarney also took into account other charges of grievous bodily harm and sexual assault.
McCarney was in a relationship with Millie's mother Rachael Martin when the 15-month-old toddler was killed over three years ago.
She died from severe head injuries in a Belfast hospital in the early hours of 11 December 2009.
During the murder trial, the court heard how Millie had sustained 21 fractured ribs, seven of which were old injuries.
CCTV footage released by police showed the moment McCarney rushed the toddler into the Accident and Emergency at Erne Hospital.
On Friday, Mr Justice Stephens said Millie was particularly young, totally helpless and completely vulnerable, and McCarney could have been in "no doubt about as to her fragility and defencelessness".
He said it was necessary to take account of a breach of trust which occurred and the element of planning necessary to ensure McCarney was alone with Millie.
Mr Justice Stephens said that Millie's death was "not a result of a child trying the patience of an adult".
He said that Millie had not been crying but was lying quietly and placidly in her cot.
The Judge said McCarney had encouraged Ms Martin to leave him alone with Millie with the intention of committing a "sadistic sexual assault" and that her head injury was likely a spontaneous response to her crying out in pain.
He said, however, that spontaneity had to be seen in the context of injuries Millie had suffered previously.
If (McCarney) had have been half a man, he would have gone into court and told the jury and (wouldn't) leave everything unanswered.
Noel Graham, Millie's grandfather
Commenting on the impact of Millie's death on her family, Mr Justice Stephens said "no one could fail to be moved by the palpable anguish, heartfelt loss and enduring emotional scars" which had been caused.
He added that the family did not even have the consolation of an honest explanation or expressions of remorse because the defendant continued to maintain that he was innocent of the offences and to be immune to the suffering of the family.
McCarney, who denied the charges, never spoke and refused to testify during the ten week trial.
It took the jury just under three hours to reach a unanimous verdict at Dungannon Crown Court in December.
Ms Martin was cleared of charges of allowing her daughter's death and cruelty.
Following the sentencing, she said she didn't think McCarney's sentence was long enough but added she was happy he was behind bars.
"It wasn't long enough, life should be life," Ms Martin's mother Margaret Graham added.
"He should never see the light of day again.
"We won't ever see Millie, her mummy will never see her wee daughter."
Millie's grandfather, Noel Graham, thanked Ms Martin's legal representatives and the judge and jury.
"We've been handed a life sentence which will never go away, but I suppose we're happy first of all that justice has been done for Millie," he added.
"His so-called calls of innocence, they don't go very far when you heard the comments by the judge today."
Outside court, Barry McCarney's father, Kevin, said they would be appealing the conviction and maintained that his son was innocent.