Isolated microgrids with green hydrogen storage offer a promising solution for supplying electricity to remote communities where conventional grid expansion is infeasible. Designing such systems requires balancing two conflicting objectives: minimizing installation and operation costs while maximizing supply reliability. This paper proposes a multi-objective optimization methodology, based on the Non-dominated Sorting Genetic Algorithm II, to determine the optimal sizing of multiple microgrid components. This sizing explicitly addresses both the power capacities (kW) (for photovoltaic panels, wind turbines, electrolyzers, and fuel cells) and the energy storage capacities (kWh and kg) (for batteries and hydrogen tanks, respectively), aiming to generate Pareto-optimal solutions that explore this trade-off. The proposed method evaluates the trade-off by minimizing two objectives: the Net Present Value, which includes investment, replacement, and maintenance costs, and the total expected interruption hours, derived from an hourly energy balance analysis. The methodology’s effectiveness is validated using four distinct case studies. Three of these are based on real locations with specific load profiles and climate data. To test the method’s robustness, a fourth case study uses a fictitious load profile, designed with pronounced seasonal variations and a clear distinction between weekday and weekend consumption. Our results demonstrate the method’s ability to identify efficient hybrid renewable topologies combining photovoltaic and/or wind generation, batteries, and hydrogen systems (electrolyzer, storage tank, and fuel cell). The obtained cost–reliability curves provide practical decision-support tools for system planners.