  Local SU(5) F-theory models lead naturally to Yukawa couplings for the third
generation of quarks and leptons, but inducing Yukawas for the lighter
generations has proven elusive. Corrections coming from gauge fluxes fail to
generate the required couplings, and naively the same applies to instanton
effects. We nevertheless revisit the effect of instantons in F-theory GUT
constructions and find that contributions previously ignored in the literature
induce the leading non-perturbative corrections to the Yukawa couplings. We
apply our results to the case of 10 x 5* x 5* couplings in local SU(5) F-theory
GUTs, showing that non-perturbative effects naturally lead to hierarchical
Yukawas. The hypercharge flux required to break SU(5) down to the SM does not
affect the holomorphic Yukawas but does modify the profile of the
wavefunctions, explaining the difference between the D-quark and lepton
couplings at the unification scale. The combination of non-perturbative
corrections and magnetic fluxes allows to describe the measured lepton and
D-quark masses of second and third generations in the SM.
