The in silico design of novel complex materials for energy conversion requires accurate, ab initio simulation of charge transport. In this work, we present an implementation of constrained density functional theory (CDFT) for the calculation of parameters for charge transport in the hopping regime. We verify our implementation against literature results for molecular systems, and we discuss the dependence of results on numerical parameters and the choice of localization potentials. In addition, we compare CDFT results with those of other commonly used methods for simulating charge transport between nanoscale building blocks. We show that some of these methods give unphysical results for thermally disordered configurations, while CDFT proves to be a viable and robust approach.