We define an analogue of the shortest-path distance for graphons. The proposed method is rooted on the extension to graphons of Varadhan's formula, a result that links the solution of the heat equation on a Riemannian manifold to its geodesic distance. The resulting metric is integer-valued, and for step graphons obtained from finite graphs it is essentially equivalent to the usual shortest-path distance. We further draw a link between the Varadhan distance and the communicability distance, that contains information from all paths, not just shortest-paths, and thus provides a finer distance on graphons along with a natural isometric embedding into a Hilbert space.