We present the conservative dynamics of compact binaries to third order in the post-Minkowskian approximation in a theory that extends general relativity by a massless scalar field coupled to the Gauss-Bonnet invariant. We employ the effective field theory approach to construct the effective action of binary systems by integrating out the metric and scalar degrees of freedom that mediate the gravitational interactions between the two bodies. We derive analytical expressions for the scattering impulse and the deflection angle to third order in the post-Minkowskian expansion. Our results are found to be in agreement, in the overlapping regimes, with state-of-the-art calculations in the post-Newtonian/post-Minkowskian theory.