This paper investigates the failure mode and the damage mechanism of steel-concrete composite slabs under high cycle fatigue loads by using three-dimensional nonlinear finite element analysis. The applicability of the simulation system, which was originally developed for reinforced concrete slabs, is extended to the steel-concrete composites with the proposed interface element, and experimentally verified with fatigue loading tests for bridge decks. The computed midspan deflection of composite slabs shows a fair agreement with data obtained from the experiment, and the horizontally induced cracking observed in reality is properly reproduced by the computational simulation. Finally, the authors predict the ultimate state at which the upper concrete layer separated by horizontal cracks fails in compression fatigue, and the corresponding S-N diagram is computationally predicted for the future discussion.