We formulate lattice perturbation theory for gauge theories in noncommutative geometry. We apply it to three-dimensional noncommutative QED and calculate the effective action induced by Dirac fermions. In particular "parity invariance" of a massless theory receives an anomaly expressed by the noncommutative Chern-Simons action. The coefficient of the anomaly is labelled by an integer depending on the lattice action, which is a noncommutative counterpart of the phenomenon known in the commutative theory. The parity anomaly can also be obtained using Ginsparg-Wilson fermions, where the masslessness is guaranteed at finite lattice spacing. This suggests a natural definition of the lattice-regularized Chern-Simons theory on a noncommutative torus, which could enable nonperturbative studies of quantum Hall systems.