This study presents a comprehensive numerical investigation into the thermal performance of solar collectors integrated with encapsulated phase change materials (PCMs) using a transient three-dimensional (3D) approach. The performance of two distinct PCMs—paraffin wax and RT60—was evaluated under varying operational conditions, including seasonal variations, inlet pipe velocities, and inlet temperatures. The results indicate that paraffin wax exhibits a higher peak temperature, reaching approximately 360 K, compared to RT60’s peak of 345 K, making paraffin wax more effective for consistent thermal energy storage. Paraffin wax also maintained higher fluid fractions, with a maximum of 0.9 in summer, indicating superior heat absorption and retention capabilities. In contrast, RT60 demonstrated a quicker phase transition, fully liquefying at a lower fluid fraction, which is advantageous for rapid heat release. Seasonal variations significantly impacted system efficiency, with the highest efficiency observed in June at 365 K and the lowest in December at 340 K. The study also found that lower inlet velocities (e.g., 0.25 L/s) significantly improved heat retention, resulting in higher outlet temperatures, while increasing the inlet temperature from 290 K to 310 K led to a marked increase in outlet temperatures throughout the day. These findings underscore the importance of optimizing PCM selection, inlet velocity, and temperature in enhancing the performance of solar thermal systems, offering quantitative insights that contribute to the development of more efficient and reliable renewable energy solutions.