When a high-speed train passes through a hood-shaped short structure (the length along the railway is typically several times as long as the diameter of its cross section), such as an overpass or a snow shelter, “structure-passing waves (SPW),” which are a type of low-frequency noise, radiate from both openings of the structure toward the outside area. The SPW could create an environmental problem of a low-frequency noise along the tracks as train speeds increase, for it steeply grows in proportion to the third or fourth power of the train speed. In this study, model experiments and acoustic analyses were conducted to investigate the generation mechanism of SPW. The run-time required for the present method of analyses is a few seconds, as opposed to the several hours typically required for an entirely numerical approach. The results of the acoustic analyses, based on a method for predicting a compression wave within a hood-shaped structure generated by a passing train, generally agree well with the experimental results of SPW with some exceptions. This implies that SPW can be modeled as a superposition of the pressure waves radiating from both openings of the structure. In addition, our model experiment and acoustic analysis show that the magnitude of SPW tends to depend on train nose/tail profile.