Many products in the chemical and agricultural industries are pelletized in the form of rod-like particles that often have different aspect ratios. However, the flow, mixing, and segregation of non-spherical particles such as rod-like particles are poorly understood. Here, we use the discrete element method (DEM) utilizing super-ellipsoid particles to simulate the flow and segregation of rod-like particles differing in length but with the same diameter in a quasi-2D one-sided bounded heap. The DEM simulations accurately reproduce the segregation of size bidisperse rod-like particles in a bounded heap based on comparison with experiments. Rod-like particles orient themselves along the direction of flow, although bounding walls influence the orientation of the smaller aspect ratio particles. The flow kinematics and segregation of bidisperse rods having identical diameters but different lengths are similar to spherical particles. The segregation velocity of one rod species relative to the mean velocity depends linearly on the concentration of the other species, the shear rate, and a parameter based on the relative lengths of the rods. A continuum model developed for spherical particles that includes advection, diffusion, and segregation effects accurately predicts the segregation of rods in the flowing layer for a range of physical control parameters and particle species concentrations.