We construct a bound state of three 1/3-quantized Josephson coupled vortices in three-component superconductors with intrinsic Josephson couplings, which may be relevant with regard to iron-based superconductors. We find a Y-shaped junction of three domain walls connecting the three vortices, resembling the baryonic bound state of three quarks in QCD. The appearance of the Y-junction (but not a ∆-junction) implies that in both cases of superconductors and QCD, the bound state is described by a genuine three-body interaction (but not by the sum of two-body interactions). We also discuss a confinement/deconfinement phase transition.