The three‐dimensional nonlinear kinetic equation for low collisionality tokamak plasmas with consistent consideration of neoclassical effects is obtained using an approach differing from the standard neoclassical theory technique. This allows treatment of large banana widths and large inverse aspect ratios. The equation is suitable for computer modeling of bootstrap currents and other phenomena arising from non‐Maxwellian distributions. The formalism described in this paper, which is for noncanonical variables, might also be of use for the consistent derivation of three‐dimensional kinetic equations that treat other effects, for example, additional heating.