Aims. The aim of this work is to investigate and characterise particle behaviour in a 3D magnetohydrodynamic (MHD) model of a reconnecting magnetic separator. Methods. We use a relativistic guiding-centre test-particle code to investigate electron and proton acceleration in snapshots from 3D MHD separator reconnection experiments, and compare the results with findings from an analytical separator reconnection model studied in a previous investigation. Results. The behaviour and acceleration of large distributions of particles are examined in detail for both analytical and numerical separator reconnection models. Accelerated particle orbit trajectories are shown to follow the separator before leaving the system along the separatrix surface of one of the nulls (determined by particle species) in the system of both models. A sufficiently localised electric field about the separator causes the orbits to appear to follow the spine bounding the separatrix surface field lines instead. We analyse and discuss the locations and spread of accelerated particle orbit final positions, which are seen to change over time in the numerical separator reconnection model. We deduce a simple relationship between the final energy range of particle orbits and the model dimensions, and discuss its implications for observed magnetic separators in the solar corona.