At least two people have died from the virus in the eastern Congolese city of Goma, near the Rwandan border.
It is one year today that DR Congo declared what has become its worst outbreak, with more than 1,800 people dead and over 2,700 infected.
The outbreak is the most complicated ever as it is happening in an active conflict zone, BBC Africa correspondent Anne Soy says.
Immigration sources in Rwanda said the border crossing point at Goma was shut on Thursday morning. This was later confirmed by DR Congo officials.
In a statement, the Congolese presidency said there had been a "unilateral decision by the Rwandan authorities" to close the crossing.
Earlier this week an artisanal miner became the second person in Goma to be killed by the disease.
He came from the north-eastern province of Ituri and had been admitted to a health centre in Kiziba, on the outskirts of Goma, on 13 July.
He later developed symptoms of bleeding and bruising, and tested positive to Ebola on Tuesday. He died on Wednesday morning.
AFP news agency has also reported that a third person - believed to be the miner's daughter - died afterwards.
Last week, the World Health Organization designated the outbreak a global health emergency.
It is the highest level of alarm the WHO can sound and has only been used four times previously - including during the Ebola epidemic that devastated parts of West Africa from 2014 to 2016, and killed more than 11,000 people.
