Getting around South Sudan is genuinely hard. The country has almost no paved roads outside of Juba and the Nimule highway. Everything else is dirt track, and much of it is seasonal.
In Juba, taxis and motorcycle taxis (boda-bodas) are the main options. Hire a private car with driver for anything beyond the city center — it is safer and more reliable. Avoid walking at night anywhere in the city.
Outside Juba, you need a 4x4 vehicle, a reliable local contact, and a current security assessment for your route. Many areas that are technically accessible on a map are not accessible in practice due to conflict, flooded roads, or the simple absence of fuel. UN and NGO convoys often travel with armed escorts.
Domestic flights connect Juba to a handful of regional towns — Wau, Malakal, Rumbek, and others — when the security situation permits. These routes are operated by small charter airlines and the schedules are unreliable. Book through a local agent or your organization's logistics team if you have one.
River travel is possible on sections of the White Nile, but is slow, logistically complicated, and requires local knowledge. There are no passenger services aimed at travelers.
The honest advice is: if you don't have a specific organization or contact managing your logistics outside Juba, don't go outside Juba.