The U.S. Embassy in Khartoum said there were several large protests throughout the capital region last weekend.
"Because even peaceful demonstrations can turn confrontational and become violent, U.S. citizens are advised to avoid all public demonstrations and political rallies as well as areas around them," an advisory read.
The warning comes amid heightened concern about the human rights situation in the region. Rupert Colville, a spokesman for the U.N. High Commissioner for Human Rights, said the agency is concerned by the growing number of attacks on human rights defenders in South Sudan.
In Sudan, Colville said four students died during clashes with police in Khartoum recently. Several others have are missing after protesting tuition increases.
"We stress the need for swift investigations into the circumstances surrounding the murders of the students and the importance of bringing the perpetrators to justice," he said in a statement.
South Sudan became an independent country last year as part of a peace deal that ended a long civil war. Both countries have teetered on the brink of war, however, amid ethnic fighting and border disputes.