The direct measurement of flexoelectric coefficients in epitaxial thin films is an unresolved problem, due to the clamping effect of substrates which induces a net strain (and hence parasitic piezoelectricity) in addition to strain gradients and flexoelectricity. Herein, we propose and demonstrate the use of van der Waals epitaxy as a successful strategy for measuring the intrinsic (clamping-free = flexoelectric coefficients of epitaxial thin films. We have made, measured, and compared ${\mathrm{BaTiO}}_{3}$ and ${\mathrm{SrTiO}}_{3}$ thin film capacitor heterostructures grown both by conventional oxide-on-oxide epitaxy and by van der Waals oxide-on-mica epitaxy, and found that, whereas the former is dominated by parasitic piezoelectricity, the response of the latter is truly flexoelectric. The results are backed by theoretical calculations of the film-substrate mechanical interaction, as well as by direct measurements that confirm the strain-free state of the films. van der Waals epitaxy thus emerges as powerful new tool in the study of flexoelectricity and, in particular, they finally allow exploring flexoelectric phenomena at the nanoscale (where strain gradients are highest) with direct experimental knowledge of the actual flexoelectric coefficients of thin films.