Constructing underpasses in operational railways is challenging due to the need for continuous train operation, minimized possession time, and controlled costs and risks. This study presents a systematic techno-economic framework for evaluating underpass construction methods on active lines, using the high-traffic Tehran–Isfahan corridor as a case study. Six common methods—cast-in-place concrete, precast concrete box, precast steel arch, concrete pile with steel deck, concrete pile with concrete deck, and concrete pile with in-situ girder and precast slabs—were compared based on cost, duration, possession time, execution risk, and socio-environmental costs of line blockage. The analysis comprises three stages: (1) Benefit–Cost (B/C) ratio, (2) sensitivity analysis with ±20% variations, and (3) multi-criteria decision-making using a combined AHP-TOPSIS method for weighting and ranking. Data were sourced from actual projects (documentation of Kashan and Shazand along the Tehran–Isfahan corridor) based on the 2024 national rate schedule. Results identified the concrete pile with in-situ girder and precast slab system as optimal, achieving a B/C ratio of 1.80, the shortest possession time (<6 hours), and the highest TOPSIS closeness coefficient (0.88). Sensitivity analysis confirmed robustness. Findings indicate that this integrated approach, while accounting for social and environmental impacts, significantly reduces costs, enhances safety, and improves productivity in active railway underpass projects.