The WHO said that Dr. Richard Valery Mouzoko Kiboung, an epidemiologist it had deployed to help rein in the Ebola outbreak, was killed in the attack on Butembo University Hospital.
Two other people were also injured but believed to be in a stable condition, it said.
The attack is the latest in a string of assaults on teams grappling with a near nine-month-old Ebola outbreak that has claimed almost 850 lives.
"I and all of WHO are deeply saddened by the loss of our colleague and brother Dr Mouzoko," WHO chief Tedros Adhanom Ghebreyesus said in a statement.
"He put himself on the frontline to save lives in the Democratic Republic of the Congo," he said, adding that "We grieve with his family and friends at this very difficult time."
Police and local officials said the victim was a Cameroonian national.
"The attack took place at the University Clinics Hospital of Butembo," said the city's mayor, Sylvain Kanyamanda.
"The (Ebola) response team was in a meeting. Armed Mai-Mai (militiamen) arrived and fired on people. A doctor, an epidemiologist, was shot and taken to the emergency room. His colleagues were injured. The doctor, a Cameroonian, later died," Kanyamanda said.
Tedros said Mouzoko's killing was "a tragic reminder of the risks health workers take every day to protect the lives and health of others."
"We are outraged by this attack: health workers and health facilities must never be targets," he insisted.
The WHO Director-General said his agency was currently "assessing the security situation to ensure the safety of all patients, health workers and Ebola responders."
"At the same time, we remain committed to continue supporting the Ministry of Health of DRC to end this outbreak as quickly as possible," he said.
The DR Congo declared a tenth outbreak of Ebola in 40 years last August in northeastern North Kivu province before the virus spread into the neighbouring Ituri region.
The epicentre of the outbreak was first located in the rural area of Mangina, but then switched to the town of Beni.
Local organisations say the number of Ebola deaths is rising.
An updated toll by the health ministry, issued on Wednesday, said there had been 843 deaths.
WHO data from April 9 put the number of confirmed or probable cases at 1,186, of which 751 had been fatal.
The outbreak is the second deadliest on record, after the epidemic that struck West Africa in 2014-16, which killed more than 11,300 people.
Efforts to roll back the highly contagious haemorrhagic fever in DRC have been hampered by fighting but also by resistance within communities to preventative measures, care facilities and safe burials.
On March 9, an attack on a treatment centre at Butembo left a policeman dead and a health worker wounded. It was the third attack on that centre.
On February 24, a treatment centre in Katwa was set ablaze.
On April 12, the WHO's Emergency Committee, in a new review of the outbreak, determined that the situation in DR Congo did not constitute a "public health emergency of international concern," a status that initiates a major global response.
Neighbouring Uganda and Rwanda, worried by the outbreak, have started vaccinating health workers. More than 102,000 people have received a new Ebola vaccine in the DRC.
Published : April 19, 2019
By : Agence France-Presse Butembo, DR Congo