The brutal murder took place in the Salem district of Tamil Nadu.
The 13-year-old's death has inflamed fears about caste-based violence in India.
According to local police, the accused Dinesh Kumar was arrested and charged under the 1989 act that criminalises caste-based violence.
Ponkarthik Kumar, a senior police official in the district, told CNN: "The girl was brutally murdered. The investigation is ongoing and the accused has been arrested."
In India, Hindus are separated into four main categories – Brahmins, Kshatriyas, Vaishyas and the Shudras.
These are then divided further into around 3,000 castes and 25,000 sub-castes, each based on their specific occupation.
According to News18, the police dismissed that the accused was mentally disturbed for beheading the young girl with a sickle.
The girl was studying at a nearby school and had parents who were labourers.
According to reports, the deceased teen had told her mum about the man's continuous sexual advances that she had turned down.
The lower castes, also known as Dalits, are often denied the right to education and employment.
They were once a community called the 'untouchables' and are deemed so unimportant that they aren't included at all in the four-fold varna system.
Despite court rulings to make the law fair for those in lower castes, activists say that deep-rooted bias remains.
Radhika Ganesh, a political activist who has been advocating for Dalit rights told CNN: "Why does the establishment not show that strength?
"Such incidents are constantly happening. When we are pushing for advocacy, the political will must be questioned, or the lack of political will must be questioned."
According to the National Crime Records Bureau, the total number of crimes against people of lower castes was more than 47,000 in 2016.
Radhika added: "The reason behind the violence is the high level of politicization of caste-based politics. Because of that there is extensive abuse of political power."
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