We present a grazing incidence fast atom diffraction (GIFAD) study of monolayer graphene on 6H-SiC(0001). This system shows a Moiré-like 13 × 13 superlattice above the reconstructed carbon buffer layer. The averaging property of GIFAD results in electronic and geometric corrugations that are well decoupled; the graphene honeycomb corrugation is only observed with the incident beam parallel to the zigzag direction while the geometric corrugation arising from the superlattice is revealed along the armchair direction. Full-quantum calculations of the diffraction patterns show the very high GIFAD sensitivity to the amplitude of the surface corrugation. The best agreement between the calculated and measured diffraction intensities yields a corrugation height of 0.27 ± 0.03 Å.