Three students from a prestigious boys school are facing sexual assault charges, accused of raping a 14-year-old girl in an alleyway.

Two 14-year-olds and a 13-year-old who attend Sydney's Scots College were arrested on Thursday over allegations stemming from July 22.

It is alleged the trio sexually assaulted the girl in an alleyway in Sydney's eastern suburbs.

Scots College said it was co-operating with police regarding the incident.

"The Scots College is aware three students are under investigation by NSW Police in relation to an alleged incident that occurred outside school hours ... the college became aware of further information through a media release issued by police (on Thursday)," the school said in a statement.

"We believe it is important the police investigation is allowed to take its course and it would not be appropriate for the college to comment further."

Police executed search warrants at a number of homes of Thursday morning before arresting the trio.

They seized electronic devices that will be forensically examined, along with replica firearms, a Glock-style BB gun, three laser pointers and an allegedly stolen number plate.

One 14-year-old and a 13-year-old were 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 three students have been granted bail and will face a children's court on August 25.

Scots College is one Sydney's most expensive schools with year 12 fees of more than $50,000 a year.

1800 RESPECT (1800 737 732)

National Sexual Abuse and Redress Support Service 1800 211 028