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Many Low and Middle Income Countries (LMICs) face intensifying climate change impacts while pursuing economic development and renewable energy goals. Among them, Nepal stands out for its abundant hydropower potential, offering a unique opportunity to produce green hydrogen for green urea synthesis, reducing fertilizer import dependence, emissions, and energy insecurity. This study adapts the Geo-X techno-economic optimization model for Nepal by integrating hydrobasin spatial geometry, distinguishing between run-of-river and reservoir hydropower plants, and incorporating economies of scale to generate realistic supply curves. Spatio-temporal modeling identifies levelized costs of hydrogen (LCOH) across basins under continuous and flexible production scenarios, with sensitivity to financing conditions. Results show that least-cost production (1–2 C/kgH2) occurs in basins with high-capacity, stable hydropower and low seasonal variability, with reservoir storage significantly reducing costs in some cases. National-scale co-optimization and grid connectivity yield 23–59 % cost savings compared to isolated basin production. Strategic site selection based namely on balancing technical efficiency of diverse renewable generation technologies, infrastructure availability, and socio-environmental considerations, emerges as essential for scaling green hydrogen and urea production in Nepal. Achieving this potential will depend on concessional financing to reduce capital costs for developers, targeted transmission network expansion, and clear production targets/use, ensuring alignment with both energy and agricultural priorities.