Chiranjibi Adhikary, a district official said on Saturday that one of the Maoists opened fire on the protesters, killing the boy.
The strike was called by a local group which said the country's interim constitution had little to offer for the development of people living in its impoverished southern plains.
Vehicles burnt after shooting
Following the incident, protesters torched several vehicles in the area, prompting authorities to impose a night curfew.
"The situation is normal now and no fresh incident of violence has been reported," Adhikary said.
Nepal's new multi-party government, formed after King Gyanendra returned power to political parties last April, regretted the clash and appealed for calm.
The country's Maoist rebels this week joined a provisional parliament, ending a decade-old conflict against Nepal's monarchy which killed more than 13,000 people.