The UN secretary general first visited Goma, the capital of North Kivu province which is trying to roll back an epidemic of Ebola that has claimed more than 2,000 lives in a year.
Guterres was received by Leila Zerrougui, his special representative in DR Congo.
The two did not shake hands, in line with health protocols aimed at curbing the spread of the highly infectious and very often fatal disease.
Guterres said he had come to express his support "with the armed forces of DRC in the fight against terrorism" which represents "a threat not only for the Congo but the whole of Africa."
The UN peacekeeping mission in the country known by its French acronym MONUSCO comprises some 16,000 troops and has an annual budget of over $1 billion.
A total of 130 militias and armed groups roam the North and South Kivu provinces of DR Congo, a vast country the size of western continental Europe.
At a centre for demobilised former militia fighters in Goma, Guterres appealed to the militias to choose peace.
"It's always possible to choose peace," he said, urging all combatants to come "to a centre like this (for) a new life in peace in their home community."
He added he had heard moving testimony from people living in the bush under the illusion that by being in an armed group they could have a better life. The reality, he insisted, was that meant "a tragic life, a life without a future."
According to the Group of Experts on Congo from New York University and Human Rights Watch, armed groups killed 1,900 civilians and kidnapped more than 3,300 people in the region between June 2017 and June 2019.
- Ebola toll rising -
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The demobilisation of militias is a priority for MONUSCO, which has been present in the DR Congo since 1999.
On Sunday, Guterres will visit Beni, one of the epicentres of the Ebola epidemic, about 350 kilometres (220 miles) north of Goma.
DR Congo health officials said late Thursday that there have been "2,006 deaths (1,901 confirmed and 105 probable)" since August 2018.
It is the second-worst Ebola outbreak in history after more than 11,000 people were killed in Guinea, Sierra Leone and Liberia between 2014 and 2016.
Containment efforts have been hindered by the conflict in the country's east, as well as attacks on health workers tackling Ebola.
Guterres will visit the remote area of Mangina in the bush outside Beni, where the epidemic first broke out at the end of July 2018, visiting a treatment centre and meeting survivors and health workers.
As the battle against Ebola continues, former health minister Oly Ilunga, who stepped down after criticising plans by the UN's World Health Organization to introduce a second, unlicensed vaccine to the country, has been banned from leaving the country pending a probe into improper use of public funds, according to migration service documents seen by AFP on Saturday.
Ilunga has been questioned as part of an inquiry into the misuse of Ebola funds. Shortly before he stepped down, the minister was replaced by President Felix Tshisekedi as the head of the country's Ebola response team.
- Militia attacks -
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Apart from Ebola, Beni has been reeling under militia attacks since October 2014 with civilians and farmers bearing the brunt of the violence.
Most of the killings have been attributed to the Islamist-rooted Allied Democratic Forces (ADF) group that arose in western Uganda in 1995 and has been accused of butchering hundreds of civilians.
"We are entirely by the side of the Congolese authorities in the fight against ADF," Guterres said in Goma.
The country's armed forces Saturday put at 1,662 the number of soldiers killed since 2014 fighting the ADF in and around Beni.
ADF fighters have also targeted UN troops, killing 15 people in an attack in December.
Under the terms of its latest mandate spanning April to December this year, the UN has closed bases in the DR Congo, reviewed its intervention strategy and cut civilian staff by 764 since the beginning of July.
But in Beni, prominent locals called for the UN to beef up the capacity of its rapid intervention force.
"We want more military means to be put at their disposal to finish the ADF in Beni," mayor Bwanakawa Masumbuko said.
Guterres will end his tour in the capital Kinshasa, where he will meet Tshisekedi, who recently unveiled a new coalition government after a delay of nearly eight months.