We study a variable-coefficient Burgers equation arising in the modelling of segregation of dry bidisperse granular mixtures. The equation is subject to nonlinear boundary conditions for the particle flux. We construct a strongly implicit Crank–Nicolson type of numerical scheme for the latter equation. The scheme is benchmarked against a standard exact solution of kink type, showing second-order of accuracy and good discrete conservation properties. Two segregation problems considered in the literature are then solved and discussed. The first is the case of a linear kinetic stress profile, which renders the governing equation of constant-coefficient type, while the second is the case of a variable kinetic stress profile based on an expression fit to particle dynamics simulation data.