It will be the first meeting between presidents of the two countries since the 1979 revolution in Iran, officials told Aljazeera.net.
"I can confirm the president will meet Khatami in Geneva," the official said. Mubarak and Khatami have never met, he added.
Meanwhile, Mubarak's Wednesday meeting with Israeli Foreign Minister, Silvan Shalom, appears to have been successful.
Speaking to reporters after the one hour meeting, Shalom said: "It was a very good meeting... I'm very encouraged."
Iran severed diplomatic relations with Egypt after the 1979 revolution and criticised it for its ties with Israel, but the two countries have been making placatory noises in the recent past.
Egypt and Iran do not have full diplomatic links, but maintain representative offices in Tehran and Cairo.
An Iranian official in Tehran said the closest contact between Khatami and Mubarak had been a telephone conversation two years ago.
The naming of a Tehran street after Islambouli, who assassinated Egyptian president Anwar Sadat in 1981, has been a major sticking point in Iran's efforts to improve ties with Egypt.
Cairo has said that if the street was renamed it would remove a major obstacle to better relations.