A Ginzburg–Landau theory for multi-band mesoscopic Josephson junctions has been developed. The theory, obtained by generalizing the de Gennes matching-matrix method for the interface order parameters, allows the study of the phase dynamics of various types of mesoscopic Josephson junctions. As a relevant application, we studied mesoscopic double-band junctions also in the presence of a superconducting nanobridge interstitial layer. The results are in agreement with a microscopic treatment of the same system. Furthermore, thermal stability of the nanobridge junction is discussed in connection with recent experiments on iron-based grain-boundary junctions.