The gynaecologist was bailed for 50,000 pounds ($3,000) by the court in Manfalout, about 400 kilometres (249 miles) south of the capital Cairo.
He said he conducted the illegal procedure alone in his clinic "without any anaesthetic or nurse present", according to prosecutors quoted in local media.
The girl bled to death shortly after the operation, commonly referred to as female circumcision.
Her father filed a police complaint against the doctor after his daughter's death in late January.
Police arrested the doctor, the parents and an aunt of the victim, before freeing the relatives days later.
Known by her first name Nada in local media, the victim's death sparked an outcry online and in Egyptian media.
The National Council for Women, which first received the complaint from the authorities, called for the "maximum punishment for all who participated in this crime".
Read also: On International Day Against FGM, Egypt remains a top offender
The doctor's release on Thursday coincided with the International Day of Zero Tolerance for Female Genital Mutilation (FGM).
Dar Al Ifta, the Egyptian body tasked with Islamic religious edicts, released a statement Thursday condemning FGM, deeming it "forbidden" in Islamic law.
Egypt first banned FGM in 2008, but the practice remains rife in the conservative country with many believing it promotes women's chastity.
A 2016 survey by the United Nations Children's Fund showed that nearly 90 percent of Egyptian women and girls aged between 15 and 49 had undergone the procedure.
Doctors found guilty of performing FGM in Egypt can face seven years imprisonment but the law is not strictly enforced.
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