We work out the theory of fractional isomorphism of graphons as a generalization to the classical theory of fractional isomorphism of finite graphs. The generalization is given in terms of homomorphism densities of finite trees and it is characterized in terms of distributions on iterated degree measures, Markov operators, weak isomorphism of a conditional expectation with respect to invariant sub-$σ$-algebras and isomorphism of certain quotients of given graphons.