Fuel cells (FCs) are critical for decarbonizing the transport industry, with Life Cycle Assessment (LCA) serving as the standard evaluation framework. However, existing literature exhibits severe methodological heterogeneities and divergent system boundaries that introduce deep epistemic uncertainties. This review conducts a systematic analysis to critically harmonize FC environmental performance across the road, aviation, and maritime sectors. Quantitative synthesis reveals global warming potential (GWP) as the dominant metric. For light-duty vehicles, GWP drops to around 30 gCO₂eq/km, matching battery-electric configurations exclusively under deeply decarbonized grids. Manufacturing FC stacks and advanced storage imposes a severe upfront carbon debt, particularly prominent in heavy-duty freight (60–130 tCO₂eq). In aviation, 80–90% in-flight GWP reductions trigger massive burden-shifting, transferring 60–70% of lifecycle damages to ground-based infrastructure. Maritime FCs shrink GWP to 0.06–0.60 kgCO₂eq/kWh, strictly contingent on upstream hydrogen production. Crucially, despite long-term GWP advantages, FC pathways face systematic penalties in acidification, eutrophication, and ecotoxicity, heavily driven by platinum-group catalysts and fluoropolymer membranes. By isolating software-driven biases and database discrepancies, this work delivers an actionable methodological roadmap, establishing a policy-aligned baseline for future FC transportation sustainability frameworks.