In an update issued on Friday, the health ministry said the new case had been discovered in the conflict-wracked Beni region.
"It seems the patient was infected after being exposed to bodily fluids from a patient who had recovered from Ebola. A detailed investigation is under way along with virus sequencing to determine the epidemiological link," it said.
The announcement came just three days after the ministry had reported "major progress", saying the epidemic appeared to have been brought under control in the Beni area.
More than 500 people have died since the deadly haemorrhagic virus broke out last year in August in the North Kivu region which borders Uganda and Rwanda.
Beni had been particularly hard hit, accounting for 118 of the fatalities.
Despite hailing the progress, the ministry had warned Beni was at risk from the neighbouring areas of Katwa and Butembo, where scores of new cases have emerged this month.
Over the past 21 days, there have been 58 cases confirmed in Katwa and 16 in Butembo, the ministry said.
So far, 536 people have died as a result of the Ebola epidemic, which broke out on August 1.
Under a programme which began a week later, 82,583 people have been vaccinated against the disease, nearly two thirds of them in Beni, Katwa and Butembo.
An epidemic can only be declared over when the country has not recorded any new case of Ebola for 42 consecutive days.
International health experts have been helping out in eastern DR Congo but efforts to contain the disease have been hampered by violence in the region, where militia groups are rampant.