We present a computationally efficient method to incorporate density-functional theory into the calculation of reflectivity in low-energy electron microscopy. The reflectivity is determined by matching plane waves representing the electron beams to the Kohn-Sham wave functions calculated for a finite slab in a supercell. We show that the observed quantum interference effects in the reflectivity spectra of a few layers of graphene on a substrate can be reproduced well by the calculations using a moderate slab thickness.