"The Descendants" actor met with South Sudan's minister of defense, a regional governor and President Salva Kiir during the visit, according to a government official.
Clooney made the dangerous crossing from South Sudan into Sudan's Nuba Mountains region to meet with residents who have been forced to seek shelter in caves because of aerial attacks by Sudan's military.
Violence has flared along the Sudan-South Sudan border since South Sudan seceded last year, and some experts worry the conflict could grow. South Sudan shut down its oil industry this year after accusing Sudan of stealing its oil.
A Senate committee on Wednesday will examine the oil dispute and the limited access aid groups are being given to Sudan's southern regions. Aid experts say people who live in Sudan's Nuba Mountains will soon face a hunger crisis.
The Associated Press contributed to this report.