A way to identify the would-be zero-modes of staggered lattice fermions away from the continuum limit is presented. Our approach also identifies the chiralities of these modes, and their index is seen to be determined by gauge field topology in accordance with the Index Theorem. The key idea is to consider the spectral flow of a certain hermitian version of the staggered Dirac operator. The staggered fermion index thus obtained can be used as a new way to assign the topological charge of lattice gauge fields. In a numerical study in U(1) backgrounds in 2 dimensions it is found to perform as well as the Wilson index while being computationally more efficient. It can also be expressed as the index of an overlap Dirac operator with a new staggered fermion kernel.