We apply canonical Poisson-Lie T-duality transformations to bosonic open string worldsheet boundary conditions, showing that the form of these conditions is invariant at the classical level, and therefore they are compatible with Poisson-Lie T-duality. In particular the conditions for conformal invariance are automatically preserved, rendering also the dual model conformal. The boundary conditions are defined in terms of a gluing matrix which encodes the properties of D-branes, and we derive the duality map for this matrix. We demonstrate explicitly the implications of this map for D-branes in two non-Abelian Drinfel'd doubles.