The meeting was expected to discuss plans by the U.N. to deploy a 4,000-strong protection force in the capital Juba, as part of the U.N. peacekeeping mission. The UN has threatened an arms embargo if the government does not cooperate.
"We will ... talk about how we move forward in trying to implement peace in this country," a senior State Department official said before the meeting.
"The people of South Sudan have suffered for far too long, and the continued instability there has led almost a million refugees and a humanitarian crisis that is far beyond the abilities of even the international community to respond to," the official added.
South Sudan initially said it would not cooperate with the 4,000-strong force that will be under the command of the existing 12,000-strong U.N. mission UNMISS. Juba has since said it was still considering its position.
"We have not rejected it or accepted it, the sovereignty of the people of South Sudan will be decided by the parliament," South Sudan's presidential spokesman Ateny Wek Ateny said.
Since the world's youngest nation gained independence in 2011, oil production - by far the biggest source of government revenue - has plummeted.
Worsening violence has raised fears of a return to civil war that erupted in late 2013, which broadly ran along ethnic lines, pitting President Salva Kiir, an ethnic Dinka, against his rival and vice president Riek Machar, a Nuer.
Machar led a two-year rebellion against forces loyal to rival Kiir before the two sides reached a peace deal in August 2015. Under the deal, Machar returned to Juba in April to resume his role as vice president.
After violence flared in the capital Juba last month, Machar withdrew his forces and Kiir subsequently sacked him as vice president.
Machar was picked up by U.N. peacekeepers in neighbouring Democratic Republic of Congo a week ago with a leg injury and was handed over to authorities in Congo.
Especially of concern to Washington was an attack on a Juba hotel in July by uniformed men who killed a U.S.-funded journalist and raped civilians, including aid workers. The U.N. has launched an investigation into accusations U.N. peacekeepers in Juba failed to respond properly to the attack.
In a letter to Kerry before his visit, the Human Rights Watch group urged him to discuss rights concerns with Kenyatta. The group said it had documented 34 cases of extrajudicial killings and another 11 deaths of people last seen in state custody over alleged links with al-Shabaab militants in Nairobi and in the northeast.