A computational model for analysis of rate-dependent interface damage which leads to interface crack initiation and propagation in multi-domain structures exposed to shear type cyclic loading is presented. Modelling of interface damage, accounting generally for various stress vs. separation relations of common cohesive zone models in this type of models, is restricted here to one with an exponential relation. The model also includes viscosity and internal parameters for the interface damage to observe a fatiguelike behaviour where a crack appears for smaller magnitudes of periodical loadings in comparison to pure uploading. The computational approach, physically based on evolution of stored and dissipated energies, behind the model results in a kind of variational formulation. Moreover, solving the problem for variables characterising the elastic state of the structure, the multi-domain symmetric Galerkin boundary element method is advantageously used. Finally, the variational character of the solution requires implementation of (sequential-) quadratic programing solvers into the computer code which is fully implemented in MATLAB. The presented numerical results for a rather academic structure demonstrate the properties of the described model and enable to extend its applicability to more general problems of engineering practice.