The role of neoclassical physics in the particle and energy transport during the application of resonant magnetic perturbations (RMPs) to suppress the edge localised modes in a tokamak is analysed. The neoclassical fluxes in non-axisymmetric DIII-D equilibria with applied RMPs are calculated using the NEO code. The magnetic field provided to NEO as an input is calculated using M3D-C1 and includes the nonlinear one-fluid plasma response. Neoclassical fluxes obtained in this study are found to dramatically increase in the presence of applied RMPs, and are in same range as the total radial particle fluxes calculated in comparable RMP discharges in DIII-D [1]. This suggests that neoclassical transport plays a significant role in edge transport when RMPs are present. An increase in neoclassical fluxes during the edge-localized mode suppressed phase in DIII-D plasmas is calculated and is strongly correlated with the observation of density pump-out in the experiment.