The girl, who cannot be named for legal reasons, said her father arranged for someone to cut her with a razorblade in the hallway of their flat while her mother was out.
"I was crying and begging. I didn't want it to happen," she said in a police interview video shown to the Central Criminal Court, or Old Bailey, England and Wales's main criminal court.
But she said her father ignored her pleas and "just egged the person on".
"I was told ... to be quiet and stop struggling."
The court heard the girl was about nine when her father, a 50-year-old solicitor, organised the cutting.
"I was undressed from my waist below ... I had to lie down and the person used a razor blade in my private area," she said in the video.
"It was a few cuts, like deep cuts, that were made ... I was not given any painkilling drugs."
The girl, now 16, said the ordeal lasted around 10 minutes. She was in pain for a week but had not examined the injury because she was "too scared".
"It was a form of punishment," she said in the video. "He just said directly, 'This is what's going to happen'. And I was supposed to take it."
The girl said she was cut a second time in similar circumstances. She said she had not grasped what had happened at the time and only realised it might be FGM after learning about the issue in secondary school.
Giving evidence by video link, she said she believed her father was angry with her after wrongly accusing her of stealing some money.
She also said her father had beaten her up "quite a lot" during her childhood; he had hit her with a branch from a tree, threatened her with an iron and hit her siblings, the jury heard.
The defendant, who cannot be named for legal reasons, has denied two charges of FGM and three counts of child cruelty.
FGM has been illegal in Britain since 1985, but there has never been a successful prosecution.
The court heard the marriage of the defendant and his wife - both originally from West Africa - had collapsed.
The defendant is expected to say that the allegations are fabrications arising from "a very acrimonious divorce".