This work addresses the multipactor problem for multi-carrier operation inside rectangular waveguide based devices, by means of numerical simulations of the electron trajectories and multiplication inside the structure. Accurate field calculation and taking into account space charge effects are mandatory. For this, a PIC-FDTD method has been employed. As a result, novel software has been implemented offering the possibility of predicting multipactor in multicarrier systems for a wide variety of situations. Simulation results show that multipactor can occur even for short pulse durations if an inter-period charge accumulation is present.