Second-order (maximally) superintegrable systems in dimensions two and three are essentially classified. With increasing dimension, however, the non-linear partial differential equations employed in current methods become unmanageable. Here we propose a new, algebraic-geometric approach to the classification problem—based on a proof that the classification space for irreducible non-degenerate second-order superintegrable systems is naturally endowed with the structure of a quasi-projective variety with a linear isometry action. On constant curvature manifolds our approach leads to a single, simple and explicit algebraic equation defining the variety classifying those superintegrable Hamiltonians that satisfy all relevant integrability conditions generically. In particular, this includes all non-degenerate superintegrable systems known to date and shows that our approach is manageable in arbitrary dimension. Our work establishes the foundations for a complete classification of second-order superintegrable systems in arbitrary dimension, derived from the geometry of the classification space, with many potential applications to related structures such as quadratic symmetry algebras and special functions.