Rustom Kerawalla was charged with negligence for failing to ensure the student's safety, police in Bangalore said.
Earlier this week police also arrested the school's skating instructor and charged him with attacking the girl. The instructor has been teaching at the school since 2011 and police said officials performed no background check when they hired him.
Police say the girl was assaulted on July 2 when she left her classroom to go to the toilet. They say she is recovering from the attack.
It came after more than 4,000 people angry over alleged police inaction in the case rallied at the weekend to demand arrests.
The rape has raised questions about the safety of India's schoolchildren.