Inter-storey seismic isolation is increasingly gaining attention. One of the main related issues is the need to limit the relative displacement between substructure and superstructure, while maintaining a good seismic performance of the superstructure. As shown in some studies, fluid viscous dampers (FVDs) mounted in isolation systems are effective in reducing isolator deflection but can be harmful by amplifying inter-storey drifts and floor accelerations. Additionally, the effectiveness of FVDs for inter-storey applications was investigated only recently, and specific approaches for their optimisation and performance evaluation are missing. Therefore, this paper proposes a method for the optimal multi-objective design of FVDs, based on the definition of appropriate surrogate response models, which allows for rationally comparing the FVD effects for a wide range of dampers and structures. In particular, the optimal FVD parameters are provided in a dimensionless form, so that they can be predicted by design equations of general validity within the range of the structures analysed. This method is applied to a stock of regular structures with various vibration periods of superstructure, isolation and substructure, examining a linear and a non-linear isolation system and a set of natural records, in order to comprehensively assess the effects of FVDs and their non-linearity on the seismic performance of these structures. Finally, prediction models of optimal FVD parameters are provided based on the results obtained and are applied to three case studies as an example.