The three male students, two aged 14 and one aged 13, from Sydney's Scots College remained outside a courtroom as their cases were heard in Surry Hills Children's Court on Tuesday.
The male students are accused of sexually assaulting and sexually touching a 14-year-old girl in an alleyway in Sydney's eastern suburbs on the evening of July 22.
Court documents alleged the incident occurred during a 55-minute window on the Wednesday evening.
No pleas are required at this early stage.
Neither the accused boys nor the alleged victim can be identified for legal reasons.
But some of their names had been revealed in online comment sections, the court was told.
Judge Sue Duncombe warned media members in court about the need to protect the identities of the teenagers allegedly involved.
"This matter has obviously attracted a lot of media attention so far," Judge Duncombe said.
"There have already been some repercussions on some of the young people from being identified."
One of the boys' lawyers told online media to close comment sections under their articles, as his client's name had been published for a significant period of time before being taken down.
All children involved in criminal proceedings are required to have their identities suppressed.
None of the boys charged are required to enter a plea at this stage.
Scots College has said it is cooperating with police regarding the alleged rape.
"Scots College is aware three students are under investigation by NSW Police in relation to an alleged incident that occurred outside school hours," the school said in a statement on August 13.
After executing a series of search warrants, police said they seized electronic devices along with replica firearms, a Glock-style BB gun, three laser pointers and an allegedly stolen number plate.
One of the 14-year-olds and the 13-year-old are charged with aggravated sexual assault in the company of others and two counts of aggravated sexual touching.
The other 14-year-old was charged with aggravated sexual assault in the company of others and one count of aggravated sexual touching.
The accused trio will remain on bail until the case is next heard on October 20.
15°C