Some have camped for months waiting for promised transport to South Sudan, others have been and returned, disappointed with life in the world's newest state.
Five months after the South gained independence, the fate of hundreds of thousands of southerners living north of the border remains uncertain, particularly so as the Northern military battles borderland rebels it - and Washington - accuse Juba of supporting.
Even their numbers lack any consensus: 700,000, according to the UN, 150,000 according to Khartoum.
Most lost their Sudanese citizenship after secession on 9 July and were given nine months - until 9 April 2012 - to "regularize their status", but were not told what this means in practice.
Many have spent their entire lives in the north; dual nationality has been ruled out.
More than 350,000 people of southern origin have headed south on their own over the past year, another 130,000 with help from the UN Refugee Agency (UNHCR) and the International Organization for Migration. By the end of the year, UNHCR expects a further 140,000 to register for assisted return.
Tens of thousands still in the north, who have made the first steps to returning, selling their homes and many of their possessions, have found themselves stuck in temporary camps with limited access to basic amenities.
"The hardest thing is that nothing has changed since the independence of South Sudan," said Victor Rabbi, leader of a camp called Al-Andaluz, in Mayo near Khartoum.
"We sold everything months ago because we thought we would go back to our homeland in July. We have nothing left. Not even a job. Since independence, as South Sudanese we no longer have the right to work in the public sector or for NGOs," he said.
The camp consists of hundreds of shelters made from wood and fabric and is home to 3,600 people.
Water is brought in by mules, and two four-litre jerry cans are sold for five pounds (US$1.80), a considerable expense for the residents.
Children cannot go to school any more, as they are no longer considered Sudanese. In the absence of electricity, power cables serve as skipping ropes for the girls.
"We are waiting for someone to tell us to leave," said Rabbi.
Forty families arrived at Al-Andaluz over a year ago. In the run-up to independence, there were promises of lorries paid for by the South Sudan government.
But the conflict in the border states of South Kordofan and Blue Nile has led to the closure of all land routes between the two countries. In any case, seasonal rains also make it almost impossible to travel by road.
Since April, the journey south can only be made by river barge or train.
While six train services have been funded, departures are not easy to programme.
"The train is protected by soldiers from Sudanese army until [the railway junction at] Babanusa. Then, SPLA [South Sudanese army] soldiers take over. The train goes through areas vulnerable to attacks. The journey to [the southern railhead town of] Wau takes 17 days," said Paul Urayo, who works in the Khartoum office handling the registration of South Sudanese from the Bahr al-Ghazal region.
"It is impossible to say how long the return trip will take in such difficult conditions," Urayo said.
After independence, the local government in some states in South Sudan chartered 16 trucks to carry returnees' luggage.
Months later much of the luggage is still stuck in Al-Andaluz, held by transport companies, which say they have not yet been paid for their services by local authorities in South Sudan.
"If it goes on like this, we'll have to write off our things," said Rabbi. "Then we really will have nothing when we arrive in South Sudan to rebuild our lives."
Slow boat to Juba
The main departures point for those heading to the southern and central states of South Sudan are the near-adjacent river Nile ports of Kosti and Renk, which more or less straddle the border.
But in the absence of commercial traffic, the 12-day passage to Juba is only possible on barges operated by the International Organization for Migration (IOM), meaning an average wait of more than 100 days. According to the IOM, once barges carrying 3,000 people leave Kosti soon, some 8,000 to 10,000 people will still be left waiting there, with another 22,000 in Renk, on the South Sudan side of the border.
Many returnees, if they have the means to do so, double back to the north, despite the uncertainty. This is particularly the case in South Sudan states experiencing armed conflict. Some 12 percent of those who travelled to Upper Nile, Unity as well as Western and Northern Bahr el-Ghazal have returned north, according to Ismael Ibrahim, an internal displacement expert working in North Sudan's Ministry of Humanitarian Affairs.
Among them was Paul*, who arrived with his wife and three children in Unity's capital, Bentiu, to the sound of landmine explosions and clashes between government forces and rebels.
"It was too dangerous. One day, I was the victim of an ambush on the way to my job as a school teacher. I decided to come back to Khartoum," he told IRIN, adding that he plans to send his children to school in either Uganda or Ethiopia.
The stark contrast between living in a city with some semblance of amenities and trying to get by in a rural area almost entirely lacking in public services and infrastructure is another reason returnees head back north.
"I sent my wife and my children to Juba in March ," Santurino, an English teacher, told IRIN in Khartoum.
"There was no electricity or running water in their hut. My two eldest children [eight and five years old] couldn't go to school because the classes were overcrowded, and it was hard for them to understand Juba Arabic [a mix of Arabic and Kiswahili spoken in Juba], which the other children spoke.
"My children were happy to come back to Khartoum. I agree that everyone has to make sacrifices, but only if it is to build the country. But six years after the peace agreement [ending years of north-south civil war], the government has done nothing and I absolutely don't believe that there will be an improvement by April," he said.
But most southerners living in Khartoum lack the means to make such choices and some do not even believe anyone doubles back once they have headed south.
"That's just propaganda from the Khartoum government!" insisted Garang Akog Madi, who lives in Al-Youssif, a northern district of the capital.
Exactly what status the "foreign" South Sudanese will be accorded if they stay in the north after the April deadline - whether, for example, they will be allowed, like Egyptian nationals, to travel freely in and out of the country - depends on the outcome of post-secession negotiations between the two governments.
But there has been little sign of progress in these stop-start talks, which also focus, with seemingly more priority, on oil, financial arrangements, border demarcation, and the status of the Abyei region.
*Not his real name