That brings to three the number of confirmed Ebola cases. Previously, infections and deaths had been limited to the rural Bikoro health zone, almost 150 kilometers away.
A newly confirmed case in a densely populated part of the country will complicate attempts to control the outbreak.
The city of about one million people is a transport hub on the Congo River, prompting fears that the virus could now spread further, threatening the capital Kinshasa and surrounding countries.
Global teams are seeking to isolate and treat anyone who may have been exposed to the virus.
Dr Peter Salama, WHO's deputy director-general of emergency preparedness and response, said the confirmed urban case of Ebola "is a major, major game-changer in the outbreak". This new case is linked with the epicentre of the epidemic, the east of Lake Tumba. It is paramount to trace the suspect case in order to have a clearer view on how it reached the city.
For a health crisis to constitute a global health emergency it must meet three criteria stipulated by WHO: It must threaten other countries via the worldwide spread of disease, it must be a "serious, unusual or unexpected" situation and it may require immediate worldwide action for containment.
The cases before this were all from remote areas that were over 100 miles south of Mbandaka in the Equateur province.
The International Federation of the Red Cross and Red Crescent Societies said the first suspected victim was a police officer who died in a health center in the village of Ikoki-Impenge, near Bikoro.
Previously, the DRC had successfully managed the Ebola outbreaks but the hemorrhagic fever spread into an urban area is posing a major challenge to combat the outbreak. WHO has therefore revised the assessment of public health risk to very high at the national level and high at the regional level. On Wednesday, the World Health Organization delivered 4,000 injections of an experimental vaccine with proven efficacy in recent trials, with more batches expected soon.
The Ebola virus is transmitted to humans from animals and has an estimated 50-percent fatality rate, according to the WHO.
An outbreak between 2014 and 2016 in west Africa was the worst ever, and killed more than 11,000. More than 4,000 doses have arrived in Congo this week, with more on the way, and vaccinations are expected to start next week. Ebola is a highly infectious disease spread through contact with even small amounts of bodily fluid of an infected person.
The vaccine supplies will be enough to vaccinate 50 rings of 150 people, the World Health Organization said.
This is the ninth Ebola outbreak in Congo since 1976, when the disease was first identified.
A total of 514 people who may have been in contact with infected people have been notified by national health authorities and are being monitored and may be candidates for the first round of vaccines.