The Bolivian government’s concerns that are related to reducing the consumption of diesel fuel, which is imported, subsidized, and provided to isolated electric plants in rural communities, have led to the implementation of hybrid power systems. Therefore, this article presents the performance analysis in terms of energy efficiency, economic feasibility, and environmental sustainability of a photovoltaic (PV)/Stirling battery system. The analysis includes the dynamic start-up and cooling phases of the system, and then compares its performance with a hybrid photovoltaic (PV)/diesel/battery system, whose configuration is usually more common. Both systems were initially optimized in size using the well-known energy optimization software tool, HOMER. An estimated demand for a hypothetical case study of electrification for a rural village of 102 households, called “Tacuaral de Mattos”, was also considered. However, since the characteristics of the proposed systems required a detailed analysis of its dynamics, a dynamic model that complemented the HOMER analysis was developed using MATLAB Simulink TM 8.9. The results showed that the PV/Stirling battery system represented a higher performance option to implement in the electrification project, due to its good environmental sustainability (69% savings in CO2 emissions), economic criterion (11% savings in annualized total cost), and energy efficiency (5% savings in fuel energy conversion).