According to reports, the boy has been charged with three counts of aggravated indecency in company, two counts of sexual intercourse with a child under the age of 10 and one count of indecent assault, Xinhua news agency reported.
Court documents alleged that the girl was attacked between June 24 and August 16.
The boy was accused of raping the girl twice on separate occasions, and was with another 12-year-old boy when he allegedly assaulted her three times.
At a Children's Court on Thursday, the boy's defence barrister James Viney formally entered a not guilty pleas to the charges on the boy's behalf.
Viney had also applied to adjust bail conditions, that meant the boy had to reside with his parents at their home in northern Sydney, so he could attend a week holiday.
Magistrate Louise McManus granted the bail variation, and ordered that a brief of evidence be served by November.
The case has been referred to the Department of Public Prosecutions, the court heard.
The second boy has also been charged with two counts of aggravated sexual assault and sexual intercourse with a child under the age of 10.
He has been granted bail and is due to appear in court for the first time on October 20.
The matter is due for court again on November 24.
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