The newly independent South Sudan has one rail connection, entering its territory from the north. It is part of Sudan’s limited narrow-gauge railway network, extending inland from Bur Sudan (Port Sudan), on the Red Sea. The terminus is at Wau.
The line was reinstated in 2010, after being destroyed in the long civil war. The new South Sudanese government has plans to extend it to the capital Juba, and on to Uganda. In Uganda it would connect (probably at Gulu) with the existing line to Mombasa. It is hard to estimate how serious these plans are, but the new government probably does want a a second rail route into the country.
The existing lines are typical colonial railways, built for the export of minerals and agricultural products, and not as part of an African network. It is relatively easy to identify new rail routes, since they are determined by geographical constraints, and the distribution of population.
The first is a line south from Juba through Central Equatorial State, and into Uganda. It would continue via Gulu to the Uganda capital, Kampala. This is a logical link in the regional context of the East African Lakes region. (The existing line from Gulu connects northern Uganda with the Kenyan port of Mombasa, rather than with the most populated region of Uganda itself).
The second possibility is a line westwards through the Western Equatorial State. It would continue along the northern edge of the Congo basin, to Bangui, capital of the Central African Republic. There, it would connect with a planned line from Cameroon to Bangui, creating an east-west African route. An alternative route into Bangui from Nyala in northern Sudan is however under consideration. (It has the advantage of a shorter transit route to Port Sudan, but it would not link to Uganda).
The third is a line north to Khartoum through Jonglei State, shortening the present indirect route via Wau and Sennar. The line could follow the abandoned Jonglei diversion canal, east of the Sudd marshes, from Bor to Malakal. This section would be a transit route: the area is almost unpopulated. The line would then follow the Nile to Khartoum.
A fourth link east from Juba through the Eastern Equatorial State is also a pure transit route. In fact it is dependent on a planned line from a new Kenyan port at Lamu, which would avoid the populated regions of Kenya entirely. This line would enter South Sudan near Lokichoggio. The port / railway project has apparently been abandoned. The line east from Juba could in theory connect to a planned Ethiopian line Weyto – Addis Ababa, but the volume of transit traffic would probably not justify it. The border region itself is almost uninhabited, and there is no existing road.
The north-eastern corner of the Congo (Democratic Republic of the Congo) is closer to the Nile than the Congo River. To some extent Juba served as a river port for this region, and there was a proposal to build a rail line from Juba to the Congolese border town of Aba. This isolated line would have a lower priority than the other lines.
All these are international strategic rail routes: they would contribute to an African network, and provide a basic network within South Sudan itself. Additional regional rail lines are very unlikely, given the low population density (average 10-15 persons / km2, but under 5 / km2 in much of the country).
All these projects are, of course, far from the present reality. Existing infrastructure in South Sudan is minimal to non-existent: it is one of the poorest countries in the world. Parts of north-eastern Africa are as thinly populated as the Sahara. The whole region has suffered multiple humanitarian crises, famines and epidemics, accompanied by massive flows of refugees. The long civil war in Sudan was linked to the even worse war in the Congo and Great Lakes region, with millions of dead. Although it may seem utopian, planning for new infrastructure would however break with the assumption, that things will stay like that for ever.