"I worked there again knowing I was going to leave," she said. "I had to prepare my parents, sell my car. I had a life to cut off," the woman, a former assistant to Katsav, told The Times of London.
She eventually left her job, and Israel, for several months. She did not report the alleged rape, which she says happened at work.
"I thought, who would believe me? I was scared, ashamed. I didn't want anyone to know," she told The Times.
Katsav has denied her allegations.
Police, meanwhile, have investigated allegations against the president made by 10 women and said they have evidence to bring charges in four cases, The Times said. Attorney General Menachem Mazuz is expected to make a decision on an indictment by year's end, after hearing from Katsav, the newspaper said.
The Times said Katsav's brother proclaimed his innocence.
"The president feels like he is a victim of the media, the police and some of the politicians in Israel," Lior Katsav told The Times.