Soheir El-Bataa was just thirteen when a doctor performed the procedure on her in 2013, leading to her death.
Yesterday, an appeals court in the Daqahliya governorate in the Nile Delta charged both her father and the doctor with involuntary manslaughter.
Campaign groups rejoiced at the news of yesterday's conviction, after doctor Raslan Fadl and El-Bataa's father were both initially acquitted in November.
However, in the retrial, prosecutors argued that El-Bataa's father had forced her to submit to the procedure.
On Monday, Fadl was given two years in prison with hard labour, plus a fine equivalent to 60 euros.
His clinic will also be closed for one year.
El-Bataa's father was also charged with involuntarily manslaughter, but granted a suspended sentence.
This is the first successful prosecution of its kind in Egyptian history, despite the ban being brought in in 2008.
Campaigners said yesterday that this sends a message to other doctors that they are not above the law.
However, deaths due to female genital mutilation are often deliberately mis-recorded, making the problem harder to fight.
Research by the United Nations Population Fund for Egypt in 2008 found that over 90 percent of women aged 15 to 49 had undergone female genital mutilation.