Sarafian was born in July 1961 in Cyprus. In 1974, while he and his parents were on holiday in London, the Turkish military invaded North Cyprus and his family became refugees. He decided to learn Turkish so that he could challenge the Turkish state's denial of the Armenian genocide and applied to study the language in Ankara. When the Turkish Ministry of Education turned down his application to study, he went anyway, paying for his tuition by teaching English. According to a "New Yorker" profile, "coming to Turkey transformed him, in an unexpected way. The combined effect of getting to know Turkish citizens, of higher education, of maturity, and of changing Turkish politics eroded the teen-age hatred until he began to seek out opportunities for reconciliation." Sarafian attended the University of Michigan at Ann Arbor in the United States and earned his M.A. in history under the tutelage of Ronald Grigor Suny.