They are the first of more than 300 detainees expected to be released this week under a peace settlement reached in January between the rebels and the government. The first group of POWs held by the SPLA was released in March.
The peace agreement also brings the SPLA into the government on Saturday, when their leader, John Garang, will be sworn in as first vice president.
The International Committee of the Red Cross, which facilitated the prisoner transfer, said it meant to ensure humanitarian principles in the process. It said in a statement that it met privately with each of the detainees to establish that each was coming to Khartoum "of his own free will."
The ICRC had previously registered the detainees, monitored their conditions and helped them communicate with their families, the statement said.
"Over many years the ICRC has repeatedly asked the Sudanese government to grant it access to detainees under its jurisdiction. No access has yet been granted," the statement said.
It is not known how many rebel prisoners the government may be holding.
The January peace deal ended the 21-year civil war, which claimed more than 2 million lives, mostly through war-induced famine and disease. It began in 1983 and pitted Islamic-dominated Khartoum against rebels seeking autonomy and a greater share of the country's wealth for the Christian and animist south.