The 25-year-old singer was also expected to later unveil a commemorative plaque, plant a tree and address the local community at the Bomu Medical Clinic.
Dr. Anderson Kahindi, head of the clinic, said about 400 children are benefiting from the program, which provides free anti-retroviral drugs.
He said Keys has been involved since 2004. The clinic is at the Coast Provincial Hospital in Mombasa, about 275 miles southeast of Nairobi.
"She learnt about the plight of children from a medical doctor who used to work at the hospital and is now studying in the U.S.," Kahindi said.
"After the tour of the hospital she will also visit selected homes of the children who are undergoing treatment to find out how they are responding," he said.
Keys didn't speak to journalists. News of her visit spread quickly, and fans struggled to get a glimpse of the singer.