The nun was taken to hospital where she had surgery and is now in a serious condition after the raid at the Convent of Jesus and Mary School in West Bengal state's Nadia district.
In a statement the Archdiocese of Calcutta said: "After tying 3 of the 5 Sisters they entered the Principal's room and ransacked it, destroying property and taking money, a laptop and a mobile phone".
Police said the group of men were stealing from the convent in eastern India early on Saturday morning when the nun attempted to stop them.
Detectives said she was then attacked by seven or eight robbers.
The government has said it will take 'strict steps' against the attackers.
A number of the school's students and local people have taken to the streets to protest against the assault.
It's the latest in a number of high profile sexual assaults in India.