It was not immediately known if the case was related to the 2018-2020 outbreak that killed more than 2,200 people in eastern Congo, the second deadliest on record, or the flare-up that killed six this year.
A 3-year-old boy tested positive near the eastern city of Beni, one of the epicentres of the 2018-2020 outbreak, and died from the disease on Wednesday, Health Minister Jean Jacques Mbungani said in a statement.
About 100 people who may have been exposed to the virus have been identified and will be monitored to see if they develop any symptoms, he added.
An internal report from Congo's biomedical laboratory said that three of the toddler's neighbours in Beni's densely-populated Butsili neighbourhood also presented symptoms consistent with Ebola last month and died, but none were tested.
Congo has recorded 12 outbreaks since the disease, which causes severe vomiting and diarrhoea, and is spread through contact with body fluids, was discovered in the equatorial forest near the Ebola River in 1976.
"Thanks to the experience acquired in managing the Ebola virus disease during previous epidemics, we are confident that the response teams ... will manage to control this outbreak as soon as possible," Mbungani said.
It is not unusual for sporadic cases to occur following a major outbreak, health experts say. Particles of the virus can remain present in semen for months after recovery from an infection.
The disease typically kills about half of those it infects although treatments developed since the record 2014-2016 outbreak in West Africa have significantly reduced death rates when cases are detected early.
Two highly effective vaccines manufactured by Merck (MRK.N) and Johnson & Johnson (JNJ.N) have also been used to contain outbreaks since then.
The 2018-2020 outbreak, however, became as deadly as it did because the response was hampered by mistrust of medical workers by the local population as well as violence by some of the armed militia groups active in eastern Congo.
