Modeling and prediction of the dynamic behavior of thermal systems operating under intermittent energy input and variable load requirements represent one of the greatest challenges in the development of efficient and reliable renewable-based power generation technologies. In this work, a data-driven machine learning modeling framework was developed based on a modified version of the Deep Operator Network architecture where the time coordinate in the trunk net is replaced with historical data of the predicting quantity. The modeling framework can be used to accurately predict the performance of renewable-based energy conversion technologies including wind- and solar-based power plants. This novel framework was applied on a solar-thermal system that consists of a solar collection loop using a flat plate collector, a power generation loop comprising an Organic Rankine Cycle, and a thermal energy storage tank connecting both loops. Variable solar irradiance, air temperature, and power load profiles were used by the Deep Operator Network to predict the State-of-Charge and the efficiency of the thermal system for several days. The results were compared with the State-of-Charge and efficiency functions calculated using a physics-based model. For a simple operation scenario, characterized by a clear sky solar irradiance profile and constant load, the standard deviation in the State-of-Charge prediction by Deep Operator Network is below 0.9% during a seven-day prediction time horizon. For the most realistic operation scenario that considers real solar irradiance and a rough load profile, the maximum standard deviation in the predictions for the State-of-Charge and efficiency are below 6.8% and 2.5%, respectively. A comparison between Deep Operator Network and Long Short Term Memory network was also performed. In general, both networks predict very well the State-of-Charge for different data density conditions; however, a higher accuracy, with a standard deviation below 2.0%, is obtained by the Deep Operator Network during three and half days using sparser training data of 20-minute points. The same accuracy for the State-of-Charge prediction with the Long Short Term Memory network is achieved only for 14 h. Average standard deviations for the State-of-Charge prediction of 1.1% with the Deep Operator Network and 1.5% with the Long Short Term Memory network are obtained for a four-day prediction time using a denser training data of 5-minute points.