The village including the girl's family, friends and classmates will be under quarantine for 21 days. The area where she died had not registered an Ebola case in nearly six months.
"They are classified as high risk although they have not exhibited any signs and symptoms of the disease," said health ministry spokesman Seray Turay. "The surveillance team of the Ebola response centre have intensified their investigations and is working to nip the issue in the bud."
Another man died of the disease two weeks ago but officials do not think the two cases are linked.
According to the National Ebola Response Centre (NERC), 1,524 people were in quarantine across the two districts.
"It is a wake-up call that Ebola is still in the country but we have an overwhelming turnout of our partners (and) the coordination response is fantastic," said a spokesman for the local Ebola response team.
The country's president, Ernest Bai Koroma, had led celebrations at a hospital in the same city just two weeks ago. At the time Sierra Leone joined its neighbor Liberia to declare the country "Ebola free."
Residents told AFP by telephone the "once vibrant community" had become "as silent as a graveyard" with people shut in their homes.
"Not even the chirpy songs of birds are heard," said 45-year-old farmer Alimamy Sesay, whose sister is in quarantine.
"Everything is at a standstill, few people woke up this morning to go to their farms and I don't know what tomorrow will bring," said Sesay.
Emmanuel Conteh, head of the Ebola Response Centre for the district of Bombali in northern Sierra Leone, said health workers were investigating how the teenager got infected, since she had not travelled outside her community in years. Initial suspicions are that she had sex with an Ebola survivor.
"We are baffled by that possibility because the survivor in question was discharged in March, way beyond the 90-day period within which sexual transmission is said to be possible," Conteh said.
The west African outbreak of Ebola has killed more than 11,000 of 28,000 people infected since first emerging in December 2013 in Guinea, with Liberia the hardest hit.