This paper presents a combined numerical–analytical approach to consider the effects of shot-peening surface treatment on the fatigue performance of metallic parts. This approach has the advantage to take into account both the favorable and unfavorable shot-peening effects. It is constituted by three principle steps: (i) a 3D finite element active simulation of the shot-peening process; (ii) prediction of the change of the shot-peened surface properties during the applied cyclic loading; and (iii) prediction of the change of the fatigue performances for both limited and high number of cycles. An application has been carried out on the aeronautical-based nickel super-alloy material, Waspaloy. The obtained results are in good correlation with available experimental investigations results and physically consistent. This proposed approach can be used to determine the optimum shot-peening conditions.