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Parts of the border were closed after the identification of a third case of Ebola in the border town of Goma, on the Congolese border, where two people have already died.
This is the worst Ebola epidemic in the history of the country: at least 2,700 people have been infected.
The epidemic has been complicated by an area of active conflict.
About 12 new cases are reported daily in the Democratic Republic of Congo, reports the World Health Organization (WHO).
The largest crossing point between the two countries reopened after 12 pm, while a smaller one was scheduled to reopen later on Thursday.
The border was closed to "avoid unnecessary pbadage" in Goma, said Gilbert Habayarimana, mayor of Rubavu district in western Rwanda, bordering Goma.
What was the reaction?
Earlier, the Congolese presidency had declared that it "deplored[d] this decision is contrary to the opinion of WHO ".
The WHO had previously warned against trying to contain the virus by restricting movement or trade. Last week, the epidemic was described as a global health emergency, its highest level of alarm.
This designation has only been used four times before, especially during the Ebola outbreak that killed more than 11,000 people in West Africa between 2014 and 2016.
Rwandans crossing the border for work expressed their concerns.
"The closure is terrible for me Yes, Ebola is a terrible thing, but life is what matters most," Ernest Mvuyekure, a builder working in Goma, told BBC. "I'm more scared of hunger than Ebola."
Claudine Uwitonze, who works both in the Rwandan city of Gisenyi and in Goma, said: "I am so shocked now, because my life depends on the DR Congo.I'm afraid to starve because I have nothing else to do. "
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