The protests, which come amid mounting fury over sexual violence in the turbulent Himalayan region, culminated in ferocious clashes between protesters and government forces.
Protesters, who took to the streets on Monday, called for the death penalty for the man who allegedly raped the young girl. An injured demonstrator is said to be critically wounded.
Police said the child was enticed into an empty school by a neighbour and raped last Wednesday. Her mother followed her screams to find her bleeding inside a bathroom.
Police said the girl was hospitalised in a critical condition but her condition has stabilised.
Top local administrator Baseer Khan said police arrested the suspect in a village in Sumbal town and an enquiry is underway.
Protests broke out on Sunday and spread to new areas on Monday after the suspect's family produced a school-issued birth certificate giving his age as 13.
Demonstrators claimed it was a fake birth certificate produced by the family to show him as a juvenile and prevent him receiving a maximum sentence of life imprisonment.
Schools, shops, and businesses were also shut across the Muslim-majority region in response to a strike called by separatist cleric Moulana Masoor Abbas to protest the rape.
“We called for a strike today to make people aware about growing incidents of rapes in the valley. We want justice for the victim,” Mr Abbas told reporters.
The child's rape comes weeks after the suicide of a girl who police say was repeatedly raped by her own father.
A police statement said that protests had spread to northern Baramulla district where 47 security personnel and seven protesters were injured in the clashes. Officials said that across the Kashmir Valley, thousands of security forces wearing riot gear were deployed to control the swelling demonstrations.
Some protesters said they no longer had trust in authorities to ensure women and girls were kept safe as authorities issued appeals for calm after the demonstrations.
Muslim clerics in the region pledged to dedicate their Ramadan sermons to women's rights.
The Muttahida Majlis-e-Ulema, a council of Muslim religious leaders and scholars, said they wanted to tackle what they said was an increase in sexual violence in the region.
Government figures show crimes against women jumped 8 per cent to 3,168 cases in 2017 from 2,915 the previous year.
In January 2018, an 8-year-old girl was abducted, starved for a week and murdered after she was raped by several people in the southern Kathua area.
The saga sparked widespread protests in Kashmir and many Indian cities and triggered the federal government to introduce the death penalty for rapists of girls under the age of 12.
The outrage drew parallels with huge protests that came after the fatal gang rape of a female student on a bus in New Delhi in 2012.
Rape is one of the most under-reported crimes in India – with some estimates indicating 90 to 95 per cent of rape cases remain unreported.
According to government data, the number of crimes against women reported to police in India rose by 83 per cent from 2007 to 2016. Four rape complaints were reported every hour in 2016, the data showed.
The conviction rate for crimes against women in India is very low – only 18.9 per cent and the lowest in a decade – according to the latest official crime statistics from 2016. The average conviction rate for all crimes is 47 per cent.
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies