We discuss 1/2 BPS domain walls in the 3d $mathcal N=4$ supersymmetric gauge theory which is self-dual under the 3d mirror symmetry. We find that if a BF-type coupling is introduced, invariance of the BPS domain wall under the duality transformation can be explicitly seen from the classical BPS equations. It has been known that particles and vortices are swapped under the 3d duality transformations. We show that Noether charges and vortex topological charges localized on the domain walls are correctly exchanged under the 3d mirror symmetry.