The man's illness was found during monitoring contacts of his father who recently died from a Nipah infection.
India has now reported 6 Nipah virus cases in the past year, all in the hot spot area in Kerala state.
So far, there are no known links between the 2 new cases.
India's Nipah patient is from an area that has reported multiple outbreaks since 2018.
The ratings aren't intended as a detailed threat assessment and don't indicate which pathogen is most likely to trigger the next pandemic, but instead are a guide for research investment.
Tests are under way on samples from five contacts who reported symptoms.
Nipah virus, which has a high fatality rate, is a top target for countermeasure development.
State officials said the boy had eaten plum fruit from the neighborhood before his symptoms began.
Two more locally acquired dengue cases have been reported in the Florida Keys.
Researchers have raised concerns about the possibility of larger outbreaks if the virus takes hold in urban areas or if the virus becomes more transmissible to humans.
