The woman, who is now 58, said she realised the nun enjoyed it when she cried so she stopped crying when she was hit.
She lived in Nazareth House in Bishop Street, Londonderry from 1957-1969.
The inquiry is investigating abuse claims against children's residential institutions in NI from 1922 to 1995.
The witness also told the inquiry she was sexually assaulted by two foster carers she was placed with.
When she went back to the home and told the nuns, they said she was talking nonsense.
The woman's evidence also included an allegation of being lined up for baths along with 100 other young girls, and of the same water being used to wash them all.
She said she did not know she had a sibling in the home until one day, when she was six, another of the residents said to her: "I'm your big sister."
Her sister left the home aged 16, the witness claimed, and wanted to take her with her, but that she was too young to go.
She told the inquiry: "I've been trying to search for my sister for a long time since I left the convent but I just can't find her."
The woman said she also searched for her mother but has never found her either.
She said she did not know what age she was or her birthday while she lived in the home.
She also told how she discovered, three years ago, that she had three other siblings, a brother and two sisters, who had been raised by their grandparents.
On Monday afternoon, another former resident, who is now 46, told the inquiry that the nuns put the fear of God into him by locking him in a cupboard as punishment for truanting.
He said he was traumatised when a nun would not let him attend his mother's funeral.
"It was like she ripped my heart out," he said.
The Historical Abuse Inquiry also heard that children at the Sisters of Nazareth Home in Londonderry were routinely given scalding or freezing showers.
The inquiry, being held in Banbridge, County Down, is chaired by retired judge Sir Anthony Hart and is considering cases in 13 residential institutions.
Public hearings are due to finish in June 2015, with the inquiry team to report to the Northern Ireland Executive by the start of 2016.
The first female witness to give evidence to the Historical Abuse Inquiry said she was beaten by a nun until she was black and blue.