Integrated energy systems (IES)s are crucial for enhancing the economy and efficiency of power generation sources (e.g., nuclear energy) necessary to unleash American energy dominance. These systems can be integrated with thermal energy storage (TES) and intermittent renewable energies to optimize overall energy use, peak-load regulation, and demand-side responses. However, the stabilization of energy generation, transport, and utilization introduces operational complexities that exceed the challenges of managing each sub-component individually. Currently, though IESs rely on human operators for efficiency and stability, reducing human error risk and enhancing performance through automation is highly desirable. Recent advances at Idaho National Laboratory have demonstrated successful control of the Thermal Energy Distributed System (TEDS). However, the fact that these efforts depended on a simplistic Sparse Identification of Nonlinear Dynamics with Control (SINDyC) model of the experiment’s dynamics led to significant discrepancies between the physical experiment and the training trajectories, thus generating large uncertainties and rendering the model inoperable. In this paper, we present an innovative approach to address these discrepancies by quantifying uncertainties and developing a more robust model. We first generated trajectories by using first-principles physics codes to encapsulate the experiment. Next, we trained thousands of models by randomly sampling these trajectories. We then collapsed all those models into one probabilistic SINDyC by fitting a multivariate Gaussian distribution onto the resulting coefficient’s distribution. Despite its simplicity, our approach successfully produced 95% confidence intervals that captured the experimental trajectories. It even did so with a higher probability and better Upooling score across six of the seven relevant quantities of interest (QoIs), as compared to other classical approaches. Ongoing research is focusing on generating new experimental trajectories to validate this approach, and on employing Bayesian calibration to refine parametric uncertainties and guide future model development efforts.