A reliability model of Level II AFDA is proposed to analyze the wave run-up occurring by the interaction of incident waves and sloped coastal structures. The reliability model may be satisfactorily calibrated by Level III Monte-Carlo simulation. Additionally, the partial safety factors of random variables related to wave run-up can be straightforwardly evaluated by the inverse-reliability method that use influence coefficients and uncertainties of random variables, and target probability of failure. In particular, a design equation for wave run-up is derived in the same form as that of deterministic design method so that the reliability-based design method of Level I may be applied easily. Finally, it is confirmed that results redesigned by the reliability-based design method of Level I with partial safety factors suggested in this paper are satisfactorily compared with results of CEM(2006) as well as those of Level II AFDA.