When performing electrodialysis (ED) to desalinate a stream, both the energy for desalination and the energy for pumping contribute to the total energy consumption, although under typical working conditions (e.g., brackish water desalination) the latter is usually negligible. However, the energy penalty might increase when desalinating viscous mixtures (i.e., viscosity of 2–20 cP). In this work, we experimentally investigate the desalination performance of an ED-unit operating with highly viscous water-polymer mixtures. The contribution of desalination and pumping energy to the total energy consumption was measured while varying diverse parameters, i.e., salinity and viscosity of the feed, and geometry and thickness of the spacer. It was found that the type of spacer did not significantly influence the energy required for desalination. The pumping energy was higher than predicted, though in most cases minimal compared to the energy for desalination. Only when using thin spacers (300 μm) and/or highly viscous feeds (12 cP), the pumping energy accounted for 50% of the total energy for low salinity feeds. Therefore, the main contributor to the energy consumption of viscous solutions is the desalination energy, provided that large spacer thicknesses (at least 450 μm) and adequate operating conditions are utilized to limit pumping energy losses.