Entanglement entropy (EE) contains signatures of many universal properties of conformal field theories (CFTs), especially in the presence of boundaries or defects. In particular, topological defects are interesting since they reflect internal symmetries of the CFT and have been extensively analyzed with field-theoretic techniques with striking predictions. So far, however, no lattice computation of EE has been available. Here, we present an ab initio analysis of EE for the Ising model in the presence of a topological defect. While the behavior of the EE depends, as expected, on the geometric arrangement of the subsystem with respect to the defect, we find that zero-energy modes give rise to crucial finite-size corrections. Importantly, contrary to the field-theory predictions, the universal subleading term in the EE when the defect lies at the edge of the subsystem arises entirely due to these zero-energy modes and is not directly related to the modular S matrix of the Ising CFT.