The influence of the capacitor configuration in the pulse supply system for rail accelerators on its efficiency was investigated in the paper. Two different configurations were compared: the first with a parallel connection of capacitors and the second with a parallel-series connection. In both cases, the same number of capacitors was assumed. All other parameters of the device were kept constant, i.e. mass and dimensions of the armature, rail length and stator geometry. A field-circuit model was used to analyse numerically the transients for different capacitor configurations and voltage values. The model was verified experimentally.