Abstract Thermocline storage tanks are considered one of the most promising options to reduce levelized electricity costs in solar thermal power plants with a storage system. Due to thermocline degradation, the annual electricity yield of a plant with thermocline storage is always lower than the same plant with a two-tank storage system. In this way, an annual performance analysis has been carried out for different charge and discharge operation strategies in order to find out the best operation mode that minimizes the difference in annual yield between both systems. 50 MW e plants based on parabolic trough technology have been analyzed and both synthetic oil and molten salts have been used as heat transfer fluids. The simulation model has been developed with the TRNSYS© software tool and the advantages and disadvantages of specific operation strategies for both kinds of storage systems have been identified. As a result, differences in fossil fuel consumption, annual yield and startup time for power block have been obtained together with some required changes in hydraulic circuit configuration. The main advantage of these results is that they can provide a useful guideline for further economic assessment associated to thermocline storage systems.