The Central African country planned to declare an end to the epidemic on Sunday, which would have allowed its overstretched health service to concentrate on containing the coronavirus, which has infected 215 and killed 20 there.
The new Ebola case, the first since Feb. 17, was a 26-year-old man in the area of Beni, a town in eastern Congo. He developed symptoms on March 27 and died in hospital on Thursday morning, regional health authorities said in a statement.
Ebola has killed more than 2,200 since August 2018 in a volatile area of the country where rebel attacks hobbled efforts to contain it. The country is also trying to bat back a measles epidemic.
"This is now a triple emergency: vulnerable populations facing ongoing humanitarian crises, the spread of COVID-19, and now again potentially a re-emerging Ebola crisis," said Kate Moger, International Rescue Committee’s Regional Vice President of the Great Lakes region.
Ebola causes fever, bleeding, vomiting and diarrhea and spreads among humans through bodily fluids. The current outbreak has killed about two thirds of those it infected.
WHO ON ALERT
The World Health Organization (WHO) had been expecting more cases to emerge in Congo, and was primed to respond, its head Tedros Adhanom Ghebreyesus said.
The agency's top emergencies expert, Mike Ryan, said health teams on the ground were continuing to investigate 2,600 Ebola alerts across the country's two affected provinces.
"We take thousands of samples every single week, and we will continue that active surveillance right the way through," he told a news conference.
Flare-ups or one-off transmissions are common towards the end of Ebola outbreaks, and a new case does not necessarily mean that the virus will spread out of control again.
But it can stay in semen for over 550 days, researchers have said, and can be transmitted through sex long after a patient recovers.
A 'LESSON' FOR COVID-19?
Congo has suffered 10 outbreaks of the virus since it was first detected in humans near the Ebola River in 1976. The biggest was in West Africa between 2013 and 2016 and killed over 11,000 people.
Two new vaccines have had a major impact on containing the virus this time, though Islamist rebels stopped health workers from reaching some areas where the virus spread.
Late last year deadly attacks on health centers in and around the city of Beni forced aid groups to suspend operations and withdraw staff from the epidemic’s last strongholds.
For those on the frontline, like Babah Mutuza lusungu, a doctor at a health research clinic in Beni, Friday's news was a bitter blow.
"It's really a step backwards, you see today if we're going to start managing a pandemic and an epidemic at the same time, it's going to be impossible, it's going to be very difficult to manage," he said.
The WHO's Ryan said it and the Congo government were ready to respond should the Ebola situation deteriorate.
"And in that sense, maybe that's our lesson for COVID-19," he said.
"There is no exit strategy until you are in control of the situation, and you must always be ready to go back again and start again."