In this article, we first establish the Fredholm theory for the bordered contact instantons defined on the punctured Riemann surfaces with prescribed asymptotic condition near the boundary punctures. We then prove the generic mapping transversality under the perturbation of Legendrian boundary condition. We also establish their generic (0-jet) evaluation transversality results of their moduli space under the perturbations of CR almost complex structures and of Legendrian boundary conditions. These are fundamental ingredients of the construction of the moduli space of bordered contact instantons and their applications.