The latest death from the dreaded haemorrhagic virus was announced almost a year since the first cases of the outbreak were recorded on August 1 last year.
Since then the virus death toll has risen to 1,803, according to figures published on Wednesday.
"A patient who was confirmed with Ebola in Goma has died. Every measure has been taken to block the chain of transmission," said Jean-Jacques Muyembe, in charge of coordinating the fight against the outbreak.
Goma, a lakeside city of more than two million people close to the Rwanda border, had already brought in infection prevention and control measures in anticipation of the arrival of the virus.
The city has an airport with flights to the capital Kinshasa, Uganda's Entebbe and Addis Ababa, the capital of Ethiopia, as well as a port that links to Bukavu and South Kivu province.
Aruna Abedi, in charge of coordinating the Ebola response in North Kivu, the worst-hit province, said the second patient to die from Ebola in Goma had arrived at a treatment centre "11 days after falling ill".
"His was really a hopeless case, because the illness was already at an advanced stage and he died overnight Tuesday."
Abedi urged the public to respond swiftly to symptoms of Ebola and "not hide suspect cases".
"The treatment centre is not a dying room -- you have to bring the patient in early," he said.
- Public health emergency -
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The first death from Ebola in Goma, reported on July 16, sparked a wave of concern.
In that case, a man described as an evangelical preacher had travelled from Goma to Butembo, one of the towns hardest hit by the outbreak.
While there, he preached at seven churches and regularly touched worshippers, including the sick, before returning to Goma.
After his death, the UN's World Health Organization (WHO) declared the epidemic a "public health emergency of international concern", a move designed to step up the global response.
The WHO has since said a shortage in funding was finally being filled after several countries renewed pledges of financial aid.
The World Bank also announced this month it would deploy a further $300 million (269 million euros) in addition to $100 million already provided.
In Goma, the capital of North Kivu province, the mood among many is frustration and despair.
"We are carrying out the guidelines, we respect the rules (about daily handwashing and checking temperatures), but what we want is for this epidemic to end quickly," said Jonas Shukuru, a motorcycle taxi boss.
"The government has to make tackling it a priority."
- 'Risks are high -
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Fears are high that the highly contagious virus will cross the Democratic Republic of Congo's porous borders.
"Economic and human exchanges are very intense," the Central African Republic's health minister, Pierre Somse, warned last week.
"Our livestock farmers sell their cattle in DR Congo. Rebel groups and poachers go back and forth across the border. The risks are high."
As DR Congo battles to contain the virus, the country's health minister Oly Ilunga quit this month in protest over the government's response to the outbreak, which saw President Felix Tshisekedi take over the reins.
One key element will be the protection of doctors and nurses trying to contain the virus.
Attacks on health workers have had a devastating effect, with seven murdered and more than 50 seriously hurt, according to an unofficial tally.
The DR Congo Ebola epidemic is the deadliest outbreak since more than 11,000 people were killed in Guinea, Sierra Leone and Liberia between 2014-2016.