Yaakov Amitai will join a small number of Israeli diplomatic staff still in the Egyptian capital.
His predecessor Yitzhak left after protesters in September tore down a security wall around the Israeli Embassy, then stormed and trashed its offices.
Foreign Ministry officials noted that they have not yet found a new embassy building in Cairo, meaning Amitai will temporarily operate from his local residence in the city.
Cairo airport officials who confirmed Amitai's arrival Monday spoke on condition of anonymity because they were not authorized to talk to the media.
Associated Press contributed to the report