We study the method for generating the initial data of black hole systems in Gauss-Bonnet (GB) gravity. The initial data are assumed to be momentarily static and conformally flat. Although the equation for the conformal factor is highly nonlinear, it is successfully solved by numerical relaxation for one-black-hole and two-black-hole systems. The common apparent horizon is studied in the two-black-hole initial data, and the result suggests that the Penrose inequalities are satisfied in this system. This is the first step for simulating black hole collisions in higher-curvature theories.