The interpretation of semiclassical gravity as an ensemble-average of CFTs has provided much progress in understanding the factorization problem and the information paradox. In this article, we consider an averaging over boundary conditions in two-dimensional boundary conformal field theories (BCFTs). We show that the boundary averaging plays an important role not only in producing wormhole contributions but also in resolving the following problem. In general setups in AdS/BCFT, one can find unphysical solutions where branes have (self-)intersections. We show that the averaging nicely resolves this intersection problem. This provides another piece of evidence that averaging plays an important role in reproducing Einstein gravity. We also propose that the averaging provides a BCFT dual of the island model.