The Bahrain Youth Society for Human Rights said on its website that Ali Jawad Ahmed, 14, was injured after security forces used “excessive force” against demonstrators.
A police official told the state news agency BNA that the incident was being investigated, without saying how the boy was injured.
“There was no reported police action against law-breakers … at the time the boy’s death was reported, except dispersing a small group of around 10 people at 1.15am,” the agency quoted the official as saying.
Small-scale protests and clashes with security forces frequently break out in areas where the majority Shia population live after the government crushed a pro-democracy movement earlier this year.
Around 30 people were killed during the protests and ensuing crackdown.
GCC troops helped Bahrain stamp out protests it says were driven by Shia sectarian motivations and instigated by Iran. Opposition groups deny this.