The country was declared free of the virus on 7 November, and the region as a whole cleared when Liberia was pronounced Ebola-free on Thursday.
But two tests conducted on a boy who died in northern Sierra Leone proved positive for the virus, a health ministry spokesman told the BBC.
It is not clear when the boy died.
Health ministry spokesman Sidi Yahya Tunis told the BBC that the boy had died in the northern Tonkolili district. The tests were conducted by British health experts.
Close to 4,000 people died of Ebola in Sierra Leone, and 11,000 people across the region, since December 2013.
In declaring West Africa clear after the recent outbreak on Thursday, the WHO warned that the area was susceptible to small flare-ups of the virus.
Liberia was the last country to see the end of active transmission of Ebola. But it had been declared clear twice before, only for the infection to re-emerge.
A country is considered free of human-to-human transmission once two 21-day incubation periods have passed since the last known case tested negative for a second time.
Figures up to 13 January 2016
Deaths - probable, confirmed and suspected
(Includes one in the US and six in Mali)
3,955 Sierra Leone