Up-type quark masses in SU(5) F-theory models

F-theory SU(5) unification has been proposed as a scenario where the mass of the top quark is naturally large, as opposed to type II SU(5) models. We analyze this claim from the viewpoint of local SU(5) F-theory models, by explicitly computing the 10 x 10 x 5 Yukawa couplings that are developed in the vicinity of an E6 singularity. Realizing this singularity via T-branes allows for a non-trivial mass for the top quark, while lighter generations of up-type quarks still have vanishing Yukawa couplings. Nevertheless, we show that by taking instanton effects into account non-vanishing Yukawas are induced for all U-quark families, together with a hierarchical structure at the level of the superpotential. Finally, by solving for internal wavefunction profiles we compute physical U-quark Yukawa couplings and show that this F-theory scenario allows to describe the measured top quark mass, as well as the observed quotients of U-quark masses.