Ensuring access to essential services, such as clean water and electricity, is a key challenge for achieving sustainable development goals in rural areas. This study proposes a novel Brayton-Stirling combined cycle-based cogeneration system for utilizing locally available biomass waste to generate both electricity and clean water. The system employs an externally fired gas turbine, a Stirling engine, and an air–gap membrane distiller. Four operation modes—parallel-powered, fully-fired, straightforward, and by-pass—were modeled for their efficiency and output. Four operation modes can be switched by two three-way valves. Sunflower husk, identified as the most effective biomass source, enabled the system to achieve up to 160 kW of electricity and 0.7 m3/h of freshwater. The electrical and exergy efficiencies of the system peaked in the parallel-power mode, offering a practical solution for enhancing rural sustainability. Moreover, the by-pass mode maximized water production, highlighting its effectiveness in addressing water scarcity along with energy generation. Through a case study, the cogeneration system has demonstrated its capability in satisfying both rural electricity and water demands throughout the day by controlling the combination of different operation modes and parameters. Therefore, it provides a promising solution for advancing rural electrification and water purification in rural areas.