Fares was born in Bern, Switzerland, the daughter of an Egyptian father and Swiss mother. She learned Arabic while studying in Cairo for a year, graduating from Cairo University in 1986. The same year, Fares directed her first short film, Magic Binoculars, the first of several produced for Swiss television. Fares began attending New York University in 1987 to study film. In 1991, she won a prize from the Stanley Thomas Johnson Foundation for her short film Sugarblues. While at New York University, Fares was mentored by Krzysztof Kieślowski and served as the assistant director for several of his works. She took her master's degree in film studies in 1995.