Fomenko is the son of Timothy Grigorievich Fomenko (Russian: Тимофей Григорьевич Фоме́нко), an industrial engineer, and Valentina Polikarpovna (née Markova) (Russian: Валентина Поликарповна Маркова), a philologist and teacher of Russian language and literature. His parents would later co-author his works on history in 1983 and 1996. Born in Donetsk, then called Stalino, he was raised and schooled in Magadan. In 1959, his family returned to Eastern Ukraine and settled in the city of Luhansk, where Fomenko attended Secondary School No. 26. During secondary school, Fomenko participated in many competitions relating to mathematics and won several medals as a result. Also in 1959, the magazine "Pionyerskaya pravda" (Russian: Пионерская правда, "Pioneer Truth") published his first known science fiction story, "The Mystery of the Milky Way".