Rachael Martin, from Main Street, Kesh, is accused of failing to protect 15-month-old Millie from the unlawful act that caused her death on December 11, 2009. She is also charged with wilfully neglecting the child in a manner likely to cause her unnecessary suffering, between September 1, 2009, and December 12, 2009.
Her former partner, 31-year-old Barry McCarney, from Irvinestown, is accused of sexually abusing and murdering Millie.
McCarney has been on remand in Maghaberry Prison since since shorty after the toddler's death. He was not Millie's father but at the time was living with Martin in a house at Glebe Park in Enniskillen.
He is accused of sexually penetrating 15-month-old Millie with a part of his body between December 8 and 11, 2009, when he then allegedly murdered her.
He is also charged with unlawfully and maliciously causing her grievous bodily harm between December 10 and 11, and her death by an unlawful act on December 11.
The pair were due to be arraigned on the charges at Omagh Crown Court, sitting in Belfast, on Friday.
The court was told that Martin had given birth the previous night.
The case was adjourned until next month when legal applications will be heard.