We extend the Atiyah, Patodi, and Singer index theorem for first-order differential operators from the context of manifolds with cylindrical ends to manifolds with periodic ends. This theorem provides a natural complement to Taubes’ Fredholm theory for general end-periodic operators. Our index theorem is expressed in terms of a new periodic eta-invariant that equals the Atiyah–Patodi–Singer eta-invariant in the cylindrical setting. We apply this periodic eta-invariant to the study of moduli spaces of Riemannian metrics of positive scalar curvature.