The virus was discovered in bats in northern Bombali region by scientists in a joint US-West African study funded by USAID.
The finding comes two years after the end of the worst-ever Ebola outbreak that killed more than 11,000 people in Guinea, Liberia, and Sierra Leone.
But researchers say the new Bombali virus is distinct from other Ebola virus strains and it is not yet known whether it could develop into the deadly disease.
The study is part of the Predict Ebola Host Research Project in West Africa that brings together scientists from the University of California Davis and Colombia University in the US and their counterparts in Sierra Leone, Guinea and Liberia to improve understanding and preparedness for future disease outbreaks in the region.
The three West African neighbor countries were hard hit by the Ebola outbreak which began in Guinea in December 2013 before spreading to Liberia and Sierra Leone. The epidemic was declared over by the World Health Organization in 2016 after claiming over 11,300 lives out of nearly 30,000 registered cases.
The Predict Research is designed to monitor wildlife specimens for known pathogens in the wake of the West African outbreak.
In Sierra Leone, of the 241 bat specimens sampled, five tested positive of the Bomali virus.
The government said it will engage the local communities in the area to create awareness of the new strain and health safety measures.
The 2014-2016 Ebola outbreak in West Africa was caused by the Zaire virus, which was discovered in the Democratic Republic of Congo, formerly Zaire, in 1976. It is the most deadly strain known.
The Zaire virus has struck DRC nine times with the latest outbreak having been declared over on Tuesday this week by the WHO after a 10-week re-emergence that claimed 33 lives.
The Sierra Leone discovery brings to six the number of known Ebola virus strains. Others are Sudan, Tai Forest, Bundibugyo, and Reston.
The Ebola virus disease is a highly fatal hemorrhagic fever that is spread through contact with bodily fluids from infected persons and animals which include non-human primates, bats, and forest antelope.