Fomenko graduated from the Mechanics and Mathematics Faculty of Moscow State University in 1967, and in 1969 began working in the department of differential geometry in said faculty. In 1970 he defended his thesis "Classification of totally geodesic manifolds realizing nontrivial cycles in Riemannian homogeneous spaces", and in 1972 defended his doctoral thesis, "The decision of the multidimensional Plateau problems on Riemannian manifolds." In December 1981 he became a professor of the department of higher geometry and topology, and in 1992 became the head of the department of differential geometry.