In total, about 3.3 million South Sudanese had fled their homes by the end of 2016, in what has become the fastest-growing displacement of people in the world.
The 2016 report showed that the number of refugees worldwide reached 22.5 million, the most ever.
According to the report, Turkey hosts the largest number of refugees at 2.9 million, followed by Pakistan, and then Lebanon.
Developing countries are hosting the majority of the world's refugees, UNHCR reported.
There were 40.3 million people displaced inside their own countries at the end of 2016, slightly fewer than the 40.8 million at the end of 2015.
A good reflection of the new thinking is the UN's latest goodwill ambassador to refugees, Yusra Mardini, a young woman who fled Syria in 2015.
"By any measure this is an unacceptable number", UN High Commissioner for Refugees Filippo Grandi said in a statement accompanying the report.
A year ago, the village of Bidi Bidi was just that, but now it is one of the biggest refugee settlements in the world - home to more than a quarter of a million people and covering 250 square kilometres.
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Leaving aside the long-standing Palestinian refugee situation, Colombians (7.7 million) and Afghans (4.7 million) remained the second- and third-largest displaced populations, followed by Iraqis (4.2 million).
Uganda, for instance, has over the past year received more than 2,000 refugees from South Sudan each and every day - more than many European countries took in a year, NRC chief Egeland pointed out.
The UN refugee chief also voiced alarm over the rapidly deteriorating situation in South Sudan, which he said was now the world's "fastest growing refugee crisis and displacement crisis".
It also illustrates the need for countries and communities supporting refugees and other displaced people to be properly resourced and supported, the absence of which can cause instability, have consequences for life-saving humanitarian work or lead to secondary displacement.
The report showed that 84 percent of all refugees who crossed borders went to low- or middle-income countries at the end of 2016, and that roughly 1 in 3 was hosted in the poorest countries, which can least afford the burden. Syria, Iraq and Colombia - which has endured decades of conflict - had the largest number of internally displaced people.
At least 10 million people are estimated to be stateless, the United Nations report found. Only Syria witnessed a larger number of new refugees, 824,000.
Donor countries should not only take in refugees but should also help to fund poorer host countries that are severely strained by helping their neighbours, the UNCHR said. "If we fail, we will be faced with a more unstable world, where the alarming high displacement figures will only continue to increase", said Egeland. The Global Trends report is based on the UNHCR's own data, data it receives from the Internal Displacement Monitoring Centre and data received from governments.
Musa Ecweru, minister for refugees, told Anadolu Agency: "We want the global community to lift the pressure and fix the damage the refugees are putting on the limited resources in the communities that host them".
The Syrian conflict, which has killed more than 320,000 people, "is becoming a forgotten crisis", warned Grandi.