The protesters, hurling rocks and shouting slogans, had gathered on Saturday morning in the western village of Narbal on the outskirts of Srinagar as shops, businesses and public transportation shut down for a strike called by separatists challenging India's sovereignty in Kashmir, police said.
News of the boy's death drew hundreds more angry villagers to join the protests, and troops tried to disperse them with tear gas.
Relatives disputed the official account, saying the boy was killed in custody.
The boy's exact age was not immediately clear, with reports ranging from 15 to 18 years old.
In an unusual move for law enforcement in Kashmir, police quickly opened a case for murder and began investigating the boy's death.