Police used batons to break up angry crowds outside a hospital where the girl had been taken for treatment.
Teachers and security guards at the government school are being questioned over the alleged assault, police said.
The gang rape and murder of a student on a Delhi bus in December sparked protests across India.
Hundreds of people gathered to protest outside the Sanjay Gandhi hospital in the Mangolpuri area of northern Delhi as news of the alleged sex attack in a local school spread.
Protesters attacked buses and pelted police with stones.
Dr Sanjay Kumar, one of those who helped treat the girl, said her injuries were consistent with rape, reports the AP news agency.
Delhi chief minister Sheila Dikshit called the attack "shameful", reports the AFP news agency.
"Rape inside a school is a shocking incident," she said.
The protests came as India's parliament held an angry debate over the rape and murder of three sisters, aged six to 11, in the state of Maharashtra last month.
No-one has been arrested and opposition MPs criticised the slow pace of the investigation.
Home Minister Sushil Kumar Shinde said one policeman had been suspended for not acting quickly enough after they had been reported missing.
Their bodies were found in a well two days after disappeared from their school.
The issue of sexual violence against women and girls has been under intense scrutiny in India after the rape and murder of a student on a Delhi bus in December led to widespread protests.
Six people deny charges over the case which shocked the nation - five in a specially convened fast-track court.
They face the death penalty, while a juvenile charged this week could be sentenced to three years in a reform facility.
