As part of the verification and validation of a newly developed non-steady-state orbit-following Monte-Carlo code, application studies of time dependent neutron rates have been made for a specific shot in the Mega Amp Spherical Tokamak (MAST) using 3D fields representing vacuum resonant magnetic perturbations (RMPs) and toroidal field (TF) ripples. The time evolution of density, temperature and rotation rate in the application of the code to MAST are taken directly from experiment. The calculation results approximately agree with the experimental data. It is also found that a full orbit-following scheme is essential to reproduce the neutron rates in MAST.