There is an immediate need for thermoelectric materials that are cost-effective and readily accessible. It has been recognized that semiconductors utilizing selenium can play a pivotal role in surmounting the barriers to their extensive commercial utilization. In this study, we demonstrate the synthesis of n-type bismuth indium selenide thin films on a glass substrate using a thermal evaporation technique, followed by post-annealing in a tube furnace at 200 °C for different durations (ranging from 1 to 5 h) in a Se atmosphere. Our primary focus is on the morphological, structural, optical, electrical, and thermoelectric power factor of both the as-deposited and post-annealed BiInSe3 thin films for varying durations. Morphological, structural, and optical analyses of the BiInSe3 films were performed using a scanning electron microscope, x-ray diffraction, and UV-spectroscopy. Furthermore, we used thermoelectric measurements to thoroughly investigate the mechanism of thermoelectric transportation at room temperature, focusing on the Seebeck coefficient and charge carrier mobility concerning the formation of thin film nanostructures. By tailoring the post-annealing process, we have optimized the structural, optical, and thermoelectric power factor of BiInSe3 films, enabling thermoelectric devices for energy applications to achieve commercial maturity.