The Doctors Without Borders (MSF) charity said it said the new vaccine; produced by a Belgian subsidiary of Johnson & Johnson; aimed at protecting about 50,000 people over a period of four months.
More than 250,000 people in the region received doses of another anti-Ebola vaccine since last year.
DR Congo declared an Ebola epidemic in August 2018 in the conflict-wracked eastern provinces of North Kivu; South Kivu and Ituri; bordering Uganda, Rwanda and Burundi.
The highly contagious haemorrhagic fever has so far killed 2,193 people; according to the latest official figures.
Efforts to roll back the epidemic have been hampered not only by fighting; but also by resistance within communities to preventative measures, care facilities and safe burials.
Health workers battling Ebola have been attacked 300 times, leaving six people dead; and 70 wounded since the start of the year, the country’s health minister said earlier this month.
Early Thursday, about 15 people received an injection in one of two MSF centres; in the North Kivu capital of Goma, a spokeswoman for the charity said.
MSF said in a statement on Tuesday that those receiving the first dose of the new vaccine; would be asked to return to complete the process.
It said launching the programme in Goma would allow authorities “to check on the success of the two-dose vaccination in a city of one million people; in a region with a mobile population and where there have been cases in the past”.
At least two Ebola cases have been registered in Goma in July and August.
But the epicentre of the disease is about 350 kilometres (220 miles) north of Goma; in the Beni-Butembo region.
It is the DRC’s 10th Ebola epidemic and the second deadliest on record; after an outbreak that struck West Africa in 2014-16, claiming more than 11,300 lives.