The rapid expansion of renewable energy technologies in sub-Saharan Africa underscores the critical need for reliable, long-duration energy storage solutions, particularly in remote and off-grid communities. A notable example of this is the mini grid in Tsumkwe, Namibia, which has a total solar photovoltaic (PV) capacity of 304 kWp, a 300 kVA diesel generator, and over 3 MWh of battery storage. Despite this sophisticated infrastructure, only 35% of annual energy demand is supplied by renewable sources; diesel generation accounts for 65% of energy produced due to limited and degraded battery capacity. This study evaluates the techno-economic feasibility of integrating hydrogen storage for long-term energy storage in the Tsumkwe mini-grid through detailed HOMER Pro simulations of nine system configurations. The analysis encompasses battery-only, hydrogen-only, and hybrid battery-hydrogen architectures, assessing economic viability (Net Present Cost and Levelized Cost of Energy), technical performance (component utilisation, reliability, and dispatch strategy), and environmental sustainability (renewable fraction and emissions). The findings indicate that battery optimisation substantially outperforms hydrogen integration under the current techno-economic conditions. The optimised battery-only system achieved the lowest Net Present Cost of USD 2.75 million and Levelized Cost of Energy of USD 0.504/kWh, representing a 20% reduction from baseline and a 34% improvement over hydrogen-augmented configurations. Adding hydrogen storage increased the costs by 21% while delivering negligible performance improvements. The hydrogen system utilisation remained extremely low (1–7% of fuel cell capacity) due to a fundamental mismatch with diurnal cycling patterns. The analysis demonstrates that advanced battery systems represent the more feasible options for Tsumkwe’s immediate future. However, ongoing national initiatives in Namibia’s emerging green hydrogen sector may eventually create opportunities for hydrogen deployment in rural applications as technology costs decline and multi-use value chains develop.