The case -- the first in a major urban hub in the region's nearly year-old epidemic of the disease -- has sparked deep concern in neighbouring Rwanda and at the UN.
The UN's World Health Organization will convene its emergency response board on Wednesday to assess whether the outbreak should be declared a "public health emergency of international concern", a move that would step up the global response. An announcement is expected late Wednesday.
The haemorrhagic virus outbreak, the second deadliest on record, has largely been contained in remote parts of DR Congo.
But WHO chief chief Tedros Adhanom Ghebreyesus on Monday said that confirmation of an Ebola case "could potentially be a game-changer" in the epidemic.
The Goma patient has been described as an evangelical preacher who had travelled from the city 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 taking the bus back to Goma last Friday, the health ministry said.
On his return on Sunday, he went to a clinic with a fever, was diagnosed with Ebola and sent back to Butembo, which is better geared than Goma for treating the disease, it said.
"Unfortunately, I can confirm that the patient died," the governor of North Kivu, Carly Nzanzu, told reporters, adding that it happened while he was being transferred by road.
- Rwanda concerns -
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More than 1,600 people have died from Ebola since August 1, when the haemorrhagic virus erupted in North Kivu and spread to neighbouring Ituri.
Health experts fear outbreaks in major cities, where population density and high mobility make it far harder to isolate patients and trace contacts compared to the countryside.
Goma is a border city of about one million people located on the northern shore of Lake Kivu, adjacent to Rwanda.
It has a port that links to Bukavu and South Kivu province and an airport with flights to Kinshasa, the Ugandan capital Entebbe and Addis Ababa, the capital of Ethiopia.
The city abuts the Rwandan city of Gisenyi, and there is a high number of daily border crossings, involving workers and people who have jobs or homes on the other side of the frontier.
Rwanda said Monday it would step up border monitoring and urged its citizens to avoid "unnecessary" travel to the eastern DRC.
France meanwhile appointed a top immunologist Yves Levy, a former head of France's prestigious National Institution of Health and Medical Research (INSERM), to spearhead its response to the outbreak.
Paris has been under pressure to strengthen its financial contribution to the Ebola campaign.
WHO's emergencies chief Mike Ryan told reporters in Geneva on Monday that the organisation had received technical help but no financial contribution from France.
At the same Geneva meeting, British International Development Secretary Rory Stewart said: "We need French-speaking expertise and above all we're going to need a lot of money -- into the hundreds of millions of dollars -- to really get the depth of response we need."
People infected with Ebola do not become contagious until symptoms appear, which is after an incubation period of between two and 21 days.
High fever, weakness, intense muscle and joint pain, headaches and a sore throat are often followed by vomiting and diarrhoea, skin eruptions, kidney and liver failure, internal and external bleeding. In the current epidemic, the mortality rate is running at 66 percent.
The worst Ebola outbreak, striking three West African countries between 2014-2016, claimed more than 11,300 lives.