Khalid Adem, a 31-year-old Ethiopian immigrant, was sentenced in Georgia to 10 years in prison for aggravated battery and cruelty to children for the 2001 crime, which the mother said she did not discover until two years later when she took her daughter to a doctor.
Mr Adem had faced a maximum sentence of 40 years in prison.
Before the sentencing, Fortunate Adem, the mother of the girl who now is seven years old, pleaded for the maximum sentence.
"This was a violation of her rights as a child, her rights as a woman, and most of all her rights as a human being, she will never be the same," she said in the courtroom.
Equality Now, a Washington-based women's rights group, said Mr Adem was the first recorded case of female genital mutilation in the United States.
"We hope that this really raises the issue of FGM in the United States, and in Georgia," said the group's director Taina Bien-Aime.
"We don't believe this is an isolated case ... and really hope that, as sad as this is ... (it) is a call to action at all levels."
Equality Now was instrumental in getting Georgia to criminalize female sexual mutilation before Mr Adem went on trial.
The Atlanta-based Centers for Disease Control estimates that more than 160,000 women have undergone sexual mutilation in the United States, including more than 50,000 minors.
Throughout the world, more than 100 million women have been subjected to the practice, which is part of tradition in 28 African nations stretching from Senegal to Somalia.
Sexual mutilation is illegal in 16 US states and since 1997 has been prohibited by federal law for people under 18 years of age.