This paper presents a machine learning (ML)-based approach for the intelligent control of Autonomous Vehicles (AVs) utilized in solar panel cleaning systems, aiming to mitigate challenges arising from uncertainties, disturbances, and dynamic environments. Solar panels, predominantly situated in dedicated lands for solar energy production (e.g., agricultural solar farms), are susceptible to dust and debris accumulation, leading to diminished energy absorption. Instead of labor-intensive manual cleaning, robotic cleaners offer a viable solution. AVs equipped to transport and precisely position these cleaning robots are indispensable for the efficient navigation among solar panel arrays. However, environmental obstacles (e.g., rough terrain), variations in solar panel installation (e.g., height disparities, different angles), and uncertainties (e.g., AV and environmental modeling) may degrade the performance of traditional controllers. In this study, a biologically inspired method based on Brain Emotional Learning (BEL) is developed to tackle the aforementioned challenges. The developed controller is implemented numerically using MATLAB-SIMULINK. The paper concludes with a comparative analysis of the AVs’ performance using both PID and developed controllers across various scenarios, highlighting the efficacy and advantages of the intelligent control approach for AVs deployed in solar panel cleaning systems within agricultural solar farms. Simulation results demonstrate the superior performance of the ML-based controller, showcasing significant improvements over the PID controller.