Computational screening is key to understanding structure-function relationships at the nanoscale but the high computational cost of accurate electronic structure calculations remains a bottleneck for the screening of large nanomaterial libraries. In this work we propose a data-driven strategy to predict accuracy differences between different levels of theory. Machine learning (ML) models are trained with structural features of graphene nanoflakes to predict the differences between electronic properties at two levels of approximation. The ML models yield an overall accuracy of 94% and 88%, for energy of the Fermi level and the band gap, respectively. This strategy represents a successful application of established ML methods to the selection of optimum level of theory, enabling more rapid and efficient screening of nanomaterials, and is extensible to other materials and computational methods.