The outbreak is reported to have occurred in a remote forest in the northeast of the country (DRC).
More than 11,000 people died during a Ebola epidemic in west Africa during 2014. At the time, 49 deaths were linked to the virus in the DRC.
A damning report later found the majority of those lives could have been saved and that the world was “grossly underprepared” for a similar event.
The WHO said it received notice of “lab-confirmed” case of Ebola in the DRC on Thursday.
One of those killed tested positive for Ebola after suffering a haemorrhagic fever in Bas-Uele province last month, Sky News reported.
Scottish nurse Pauline Cafferkey almost died twice after contracting the virus during work in Sierra Leone.
She became the first person to be diagnosed with Ebola in the UK after arriving back in the country with colleagues in December 2014.
A series of disciplinary hearings were held after an incorrect temperature reading initially meant Cafferkey was allowed to travel home.