We extend the formalism to calculate non-Gaussianity of primordial curvature perturbations produced by preheating in the presence of a light scalar field. The calculation is carried out in the separate universe approximation using the non-perturbative delta N formalism and lattice field theory simulations. Initial conditions for simulations are drawn from a statistical ensemble determined by modes that left the horizon during inflation, with the time-dependence of Hubble rate during inflation taken into account. Our results show that cosmic variance, i.e., the contribution from modes with wavelength longer than the size of the observable universe today, plays a key role in determining the dominant contribution. We illustrate our formalism by applying it to an observationally-viable preheating model motivated by non-minimal coupling to gravity, and study its full parameter dependence.