Barry McCarney, 35, challenged verdicts that he was guilty of killing Millie Martin.
He also contested charges that he subjected her to a sexual assault and grievous bodily harm.
But in court in Belfast on Friday, senior judges refused his appeal.
They rejected criticisms about the handling of applications for "no case to answer" at his trial.
Allegations of failures in how the jury was directed were also dismissed.
Lord Justice Higgins said: "We do not consider that any of the matters relied upon by the applicant rendered his trial for the murder of Millie Martin to have been unfair."
McCarney  was ordered to serve a minimum 25 years of a life sentence imposed for killing the toddler.
She died in December 2009 after being admitted to hospital in Enniskillen, County Fermanagh, with serious injuries. She had fractured ribs, heavy bruising and a burnt finger.
McCarney, formerly of Trillick, County Tyrone, had started a relationship with Millie's mother, Rachael, and moved into the family home in Enniskillen months before her death.
Although he was found guilty of murder, no verdict was entered on a separate count of causing the death of a child.
Rachael Martin was cleared of charges of allowing her daughter's death and cruelty through wilful neglect.
Lord Justice Higgins, sitting with Lord Justice Coghlin and Mr Justice Horner, held that the trial judge had been "scrupulous" in ensuring proceedings against McCarney were fair.
He also pointed out  that McCarney declined to give evidence, unlike his co-accused, Rachel Martin.
McCarney, who appeared by video-link from prison to hear his appeal being thrown out, is now expected to press ahead with a bid to have his jail term reduced.
A man jailed for murdering his ex-partner's 15-month-old daughter has failed in a bid to have his convictions overturned.