However, the construction of an underpass beneath operational railway lines is constrained by the need to minimize track possession time, as well as by geotechnical challenges and construction limitations. The objective of this study is to identify the optimal construction method and to elucidate effective execution innovations for underpass construction under such conditions. To this end, six construction methods—including cast-in-place concrete underpasses, precast concrete box underpasses, precast steel arch sections, cast-in-place concrete piles with a precast steel deck, and cast-in-place concrete piles with an integral precast concrete deck—were compared using SWOT analysis, quantitative evaluation, and multi-criteria decision-making based on the Analytic Hierarchy Process. The composite system consisting of cast-in-place concrete piles and beams with a precast concrete slab was identified as the superior alternative, achieving a final score of 3.90 out of 5. Accordingly, the principal innovations of this method were then examined, including controlled trench excavation, the use of a reinforced block wall as a ballast guard for temporary stabilization of the track bed with rapid removability during track lifting, and the use of precast concrete slabs to stabilize the soil and prepare the foundation for deck installation. The results indicate that these execution innovations shift a substantial portion of the construction activities to the pre-possession stage and enable rapid installation of the precast deck, making it possible to construct a 12 m span underpass with a track closure of less than 6 hours and without the need for a diversion route. Therefore, the composite system of cast-in-place concrete piles and beams with a precast concrete slab can be regarded as an efficient method for the design and construction of railway underpasses beneath operational lines, particularly for spans of approximately 10 to 12 m.