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Thousands of South Sudanese are arriving each day in Uganda, which has received more than 700,000 refugees from its famine-stricken neighbour since war erupted there in December 2013.
"I've seen children tied to their dead mother and thrown in the river – soldiers have been doing this a lot," Save the Children cited one 31-year-old woman, Sylvia, as saying.
South Sudan is Africa's largest refugee crisis, with more than 1.5 million people fleeing since 2013, when President Salva Kiir fired his deputy Riek Machar, sparking a conflict that has split the world's youngest country along ethnic lines.
The United Nations declared last month that parts of South Sudan are experiencing famine, the first time the world has faced such a catastrophe in six years.
Almost nine in 10 refugees arriving in Uganda are women and children, often hungry, terrified and alone, Save the Children said.
"They are telling us that back home they have witnessed their parents being killed," one Save the Children worker said in a statement.
"One boy said his father was hung next to him - it comes to him in his dreams and the next morning he wakes up and he's speechless."
Sylvia arrived in Uganda with a two-year-old baby girl that she found by the roadside.
"I found her crying in a ditch," she told Save the Children. "She was naked, malnourished and dehydrated."
Other women told the charity they had seen women and girls being raped by up to 10 soldiers.
"The testimonies we are hearing are horrifying," Pete Walsh, Save the Children's South Sudan country director said.
"All parties to the conflict must ensure civilians are protected and aid workers are able to continue delivering life-saving healthcare and protection."
Aid workers have been unable to reach tens of thousands of people in need for months due to clashes, denial of access at checkpoints and looting of humanitarian compounds, according to the United Nations.
More than 100,000 South Sudanese are experiencing famine, with a further one million on the brink of starvation, it says. (Reporting by Katy Migiro @katymigiro; Editing by Emma Batha. Please credit the Thomson Reuters Foundation, the charitable arm of Thomson Reuters, that covers humanitarian news, women’s rights, trafficking, property rights and climate change.