We propose the use of a constraint preconditioner for the iterative solution of the linear system arising from the finite element discretization of the coupled Stokes-Darcy system. The Stokes-Darcy system is a set of coupled PDEs that can be used to model a freely flowing fluid over porous media flow. The fully coupled system matrix is large, sparse, non-symmetric, and of saddle point form. We provide for exact versions of the constraint preconditioner spectral and field-of-values bounds that are independent of the underlying mesh width. We present several numerical experiments, using the deal.II finite element library, that illustrate our results in both two and three dimensions. We compare exact and inexact versions of the constraint preconditioner against standard block diagonal and block lower triangular preconditioners to illustrate its favorable properties.