The 19-year-old education activist was visibly moved by the sobbing Burundian refugees, prompting her father Ziauddin Yousafzai to step in and respond on her behalf.
"It's extremely shocking," the world's youngest Nobel laureate, who survived a near-fatal attack by the Taliban, told the Thomson Reuters Foundation in Rwanda's Mahama refugee camp on Thursday.
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"It's very tragic their stories, very moving and emotional."
Burundi has been mired in a year-long crisis that has killed more than 450 people and forced 270,000 to flee since President Pierre Nkurunziza pursued and won a third term. Opponents said his move violated the constitution and a deal that ended a civil war in 2005.
Ange-Mireille Ndikumwenayo was on a bus heading to Rwanda in May 2015 when she saw two girls being gang raped by the roadside.
"They tried to run and asked for help but no one could help them because they had guns," said the 20-year-old, referring to the Imbonerakure, the ruling party's youth wing which rights groups say has attacked and tortured government opponents, charges it denies.
"It broke my heart."
Spies
The majority of the 50,000 Burundian refugees living in Mahama camp in southeastern Rwanda are children.
There are about 12 new arrivals each day, said the United Nations refugee agency's (UNHCR) Paul Kenya, head of Kirehe field office, often children travelling alone.
"Some are being asked now to join the political party and the militia and they are refusing and then they are forced to flee," he said.
People whose families are known to have fled to Rwanda often fall under suspicion and have to leave as well, he said.
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Almost 65 per cent of Mahama's refugees come from Burundi's border province of Kirundo as roadblocks make it difficult for people living further south to leave the country, he said.
"They were being beaten to explain why they were fleeing," he said. "They were accused of being spies."
Relations between Rwanda and Burundi are tense following a report to the UN Security Council that accused Rwanda of training and financing Burundian rebels, charges Rwanda denies.
The Burundi crisis has sparked concerns it could spiral into an ethnic conflict in a region where memories of neighbouring Rwanda's 1994 genocide are fresh.
The report said the rebels, including six children, said they had been recruited in Mahama camp, an issue that Yousafzai raised on Wednesday with Rwandan President Paul Kagame.
"It is their age to get education... not (to be) sent back as fighters to their country," she said.
UNHCR's Rwanda representative, Azam Saber, said his staff had received reports of forced recruitment among refugees, although they had not witnessed it themselves.
"In order to be a safer site, we need to keep children and adolescents busy either in school or outside school," he said, adding that he has asked the International Olympic Committee to provide the children with football and basketball pitches.
UNHCR has only received $30 million of the $105 million it has requested for 2016 for refugees in Burundi, he said, leaving tens of thousands living in worn out tents for more than a year.
Shameful
Ange-Mireille Ndikumwenayo, who witnessed the roadside gang rape, told Yousafzai how girls who gave birth after being raped felt they could not step back inside a classroom.
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"It's shameful to speak up and say that you have been raped," she said, dressed in a blue shirt and black skirt like her classmates seated on a wooden bench behind her.
"When you are not married and you give birth, you think life is over."
Ndikumwenayo became a mother three years ago but returned to school with the dream of becoming a journalist to draw attention to violence against women and girls.
She is now in her final year at Paysannat School, on a hill just outside the camp.
Eight out of ten of the school's 12,000 students are refugees, who study together with local Rwandan children.
"To learn with these Rwandan children can alleviate the stress of life that they can have," said Rwanda's minister for refugee affairs, Seraphine Mukantabana, herself a former refugee.
"They think that life can continue even if they are in exile."
The world's first university in a refugee camp opened in Kiziba camp in western Rwanda in 2015, home to 17,000 Congolese refugees, some of whom have been in exile for 20 years.
The students study online and with visiting professors from the Rwandan capital, Kigali.
"We will be establishing the second ever university in a refugee camp in Mahama very soon," the UNHCR's Saber told Yousafzai.
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