Hydrogen, known for its high energy content and clean combustion, is promising in the energy transition. This study explores the environmental impact of a solid oxide fuel cell (SOFC) system. 1 kg of hydrogen production at 1 bar serves as the functional unit. The SOFC system generates hydrogen, electricity, and heat across five modes. Results indicate that the SOFC system achieves a global warming potential of 0.17–9.50 kg CO2-eq/FU using the system expansion method. Regional analysis shows that areas with high renewable electricity shares experience increased CO2 emissions due to functional unit decision. The exergy allocation method is less sensitive to electricity sources and seasonal emission profiles than system expansion. Comparing eight production routes, the SOFC system using biomethane (−5.46 kg CO2-eq/FU) outperforms steam methane reforming (11 kg CO2-eq/FU) and biomass gasification (1.49 kg CO2-eq/FU). These insights are valuable for advancing renewable energy initiatives and effectively mitigating climate change.