Unintentional pesticide contamination in rotational crops, often caused by soil contamination from pesticide use in the preceding crops, is a major concern in a positive list system. The residue and dissipation pattern of fluopyram in soil and scallions were investigated to evaluate the uptake of fluopyram from the soil by scallions. In addition, the management concentration in soil (MCsoil) was calculated based on bioconcentration factors (BCFs) and the maximum residue limit (0.2 mg/kg) in leaf-and-stem vegetables. In a field experiment, plots in two different trials, A and B, were treated with 0.06 g fluopyram/m2and maintained for 30 days according to OECD guidelines. Scallion seedlings were cultivated for 48 days. Soil samples were taken at three different time points: DAP (Days after planting) 0, 34, and 48. Scallion samples were collected at five different time points: DAP 20, 27, 34, 41, and 48. The initial amounts of fluopyram in soil at DAP 0 were 0.94 ± 0.03 and 0.96 ± 0.04 mg/kg in trials A and B, respectively. The half-life of fluopyram in the soil was 87–231 days. Fluopyram uptake by the roots increased over time, but fluopyram residue in the scallions decreased due to the dilution effect caused by an increase in plant weight. The residues in the scallions at DAP 48 were 0.22 ± 0.01 and 0.15 ± 0.01 mg/kg in trials A and B, respectively. The BCFs of scallions for fluopyram were 0.21–0.24 (trial A) and 0.14–0.18 (trial B). The MCsoilwas proposed as 0.8 mg/kg, and may be utilized as a safe management guideline for precautionary practices to cultivate safe rotational crops.