ABSTRACT We study the potential of the kinematic Sunyaev–Zel’dovich (kSZ) effect as a probe for cosmology, focusing on the pairwise method. The main challenge is disentangling the cosmologically interesting mean pairwise velocity from the cluster optical depth and the associated uncertainties on the baryonic physics in clusters. Furthermore, the pairwise kSZ signal might be affected by internal cluster motions or correlations between velocity and optical depth. We investigate these effects using the Magneticum cosmological hydrodynamical simulations, one of the largest simulations of this kind performed to date. We produce thermal SZ and kSZ maps with an area of ≃ 1600 deg2, and the corresponding cluster catalogues with M500c ≳ 3 × 1013 h−1 M⊙ and z ≲ 2. From these data sets, we calibrate a scaling relation between the average Compton-y parameter and optical depth. We show that this relation can be used to recover an accurate estimate of the mean pairwise velocity from the kSZ effect, and that this effect can be used as an important probe of cosmology. We discuss the impact of theoretical and observational systematic effects, and find that further work on feedback models is required to interpret future high-precision measurements of the kSZ effect.